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HEADER HYDROLASE 30-JAN-20 6XYC
TITLE TRUNCATED FORM OF CARBOHYDRATE ESTERASE FROM GUT MICROBIOTA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ACETYL XYLAN ESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: METAGENOME;
SOURCE 3 ORGANISM_TAXID: 256318;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008
KEYWDS ACETYL XYLAN ESTERASE, ALPHA/BETA HYDROLASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR L.PENTTINEN,N.HAKULINEN,E.MASTER
REVDAT 1 27-JAN-21 6XYC 0
JRNL AUTH L.PENTTINEN,L.HAMELEERS,N.HAKULINEN,E.MASTER,E.JURAK
JRNL TITL CRYSTAL STRUCTURE AND CHARACTERIZATION OF AN ACETYL XYLAN
JRNL TITL 2 ESTERASE FROM BEAVER GUT METAGENOMICS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.14_3260
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.83
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 22925
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : 0.203
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1147
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 29.8300 - 3.6900 1.00 2908 153 0.1588 0.1784
REMARK 3 2 3.6900 - 2.9300 1.00 2760 146 0.1701 0.1925
REMARK 3 3 2.9300 - 2.5600 1.00 2724 143 0.1726 0.1927
REMARK 3 4 2.5600 - 2.3300 1.00 2701 142 0.1705 0.2128
REMARK 3 5 2.3300 - 2.1600 1.00 2711 143 0.1806 0.2092
REMARK 3 6 2.1600 - 2.0300 1.00 2670 141 0.1970 0.2484
REMARK 3 7 2.0300 - 1.9300 1.00 2664 140 0.2236 0.2735
REMARK 3 8 1.9300 - 1.8500 0.99 2640 139 0.2696 0.3161
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.507
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 27.03
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.76
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.005 2236
REMARK 3 ANGLE : 0.701 3047
REMARK 3 CHIRALITY : 0.047 336
REMARK 3 PLANARITY : 0.004 397
REMARK 3 DIHEDRAL : 2.546 1784
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6XYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-20.
REMARK 100 THE DEPOSITION ID IS D_1292106528.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-MAR-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9159
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22926
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850
REMARK 200 RESOLUTION RANGE LOW (A) : 29.840
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 6.984
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 11.2600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 6TKX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.35
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 30 % PEG MME
REMARK 280 5000, 0.1 M MES PH 6.0, PROTEIN CONCENTRATION 12 MG/ML, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.18900
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.78000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.78000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.28350
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.78000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.78000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.09450
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.78000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.78000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.28350
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.78000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.78000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 11.09450
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 22.18900
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 410 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10850 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 LEU A 293
REMARK 465 GLU A 294
REMARK 465 HIS A 295
REMARK 465 HIS A 296
REMARK 465 HIS A 297
REMARK 465 HIS A 298
REMARK 465 HIS A 299
REMARK 465 HIS A 300
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OD1 ASP A 192 OG SER A 194 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 GLU A 41 100.06 -54.33
REMARK 500 SER A 55 20.35 -168.16
REMARK 500 ASN A 61 20.35 -147.86
REMARK 500 SER A 128 -121.51 48.59
REMARK 500 PHE A 176 55.34 36.06
REMARK 500 VAL A 239 -56.14 -120.68
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue AES A 701
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6TKX RELATED DB: PDB
DBREF 6XYC A 8 300 PDB 6XYC 6XYC 8 300
SEQRES 1 A 293 LYS GLY PRO ALA GLU ASP THR TYR SER THR SER TRP THR
SEQRES 2 A 293 ASN VAL ASN TYR ALA SER ASP SER LEU GLU SER HIS ASN
SEQRES 3 A 293 LEU ASP ILE TYR LEU PRO LYS GLU GLN LYS THR ALA TYR
SEQRES 4 A 293 LYS ALA ILE ILE ILE ILE TYR GLY SER ALA TRP PHE ALA
SEQRES 5 A 293 ASN ASN ALA LYS ALA MET ALA SER ALA SER ILE GLY ALA
SEQRES 6 A 293 PRO LEU LEU LYS ALA GLY PHE ALA VAL ILE SER ILE ASN
SEQRES 7 A 293 HIS ARG SER SER MET GLU ALA ILE TRP PRO ALA GLN ILE
SEQRES 8 A 293 GLN ASP VAL LYS ALA ALA ILE ARG TYR VAL ARG SER ASN
SEQRES 9 A 293 ALA ALA LYS TYR ASN ILE ASP PRO SER PHE ILE GLY ILE
SEQRES 10 A 293 THR GLY PHE SER SER GLY GLY HIS LEU SER ALA PHE ALA
SEQRES 11 A 293 GLY VAL THR ASN GLY VAL LYS THR LEU THR SER GLY ASP
SEQRES 12 A 293 LEU THR VAL ASP ILE GLU GLY SER LEU GLY ASN TYR LEU
SEQRES 13 A 293 SER THR GLY SER HIS VAL ASP ALA VAL VAL ASP TRP PHE
SEQRES 14 A 293 GLY PRO VAL ASP MET ALA HIS MET SER ASN CYS VAL ALA
SEQRES 15 A 293 PRO ASN ASP ALA SER THR PRO GLU ALA VAL LEU ILE GLY
SEQRES 16 A 293 LYS LYS ASP PRO ARG GLU GLU PRO ASP TRP VAL LYS LEU
SEQRES 17 A 293 ILE SER PRO ILE ASN PHE VAL ASP LYS ASP ASP PRO ASP
SEQRES 18 A 293 ILE LEU ILE ILE HIS GLY ASP ALA ASP ASN VAL VAL PRO
SEQRES 19 A 293 HIS CYS GLN SER VAL ASN LEU LYS ASN VAL TYR ASP ASN
SEQRES 20 A 293 ALA GLY ALA LYS ALA THR PHE ILE SER VAL PRO GLY GLY
SEQRES 21 A 293 GLY HIS GLY PRO GLY CYS PHE ASP THR GLN TYR PHE LYS
SEQRES 22 A 293 ASP MET THR ASP PHE PHE THR GLU GLN SER THR LYS LEU
SEQRES 23 A 293 GLU HIS HIS HIS HIS HIS HIS
HET AES A 701 22
HETNAM AES 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
HETSYN AES AEBSF
FORMUL 2 AES C8 H10 F N O2 S
FORMUL 3 HOH *189(H2 O)
HELIX 1 AA1 ALA A 11 ASP A 13 5 3
HELIX 2 AA2 LEU A 29 SER A 31 5 3
HELIX 3 AA3 ALA A 62 ALA A 77 1 16
HELIX 4 AA4 PRO A 95 ASN A 111 1 17
HELIX 5 AA5 ALA A 112 TYR A 115 5 4
HELIX 6 AA6 SER A 128 VAL A 139 1 12
HELIX 7 AA7 ASP A 180 VAL A 188 5 9
HELIX 8 AA8 THR A 195 ILE A 201 1 7
HELIX 9 AA9 ASP A 205 GLU A 208 5 4
HELIX 10 AB1 GLU A 209 ILE A 216 1 8
HELIX 11 AB2 SER A 217 VAL A 222 5 6
HELIX 12 AB3 HIS A 242 GLY A 256 1 15
HELIX 13 AB4 ASP A 275 LYS A 292 1 18
SHEET 1 AA1 8 TYR A 15 ASN A 23 0
SHEET 2 AA1 8 ASN A 33 PRO A 39 -1 O ILE A 36 N TRP A 19
SHEET 3 AA1 8 ALA A 80 ILE A 84 -1 O VAL A 81 N TYR A 37
SHEET 4 AA1 8 TYR A 46 ILE A 52 1 N LYS A 47 O ALA A 80
SHEET 5 AA1 8 ILE A 117 PHE A 127 1 O ASP A 118 N TYR A 46
SHEET 6 AA1 8 ALA A 171 TRP A 175 1 O TRP A 175 N GLY A 126
SHEET 7 AA1 8 ILE A 229 GLY A 234 1 O LEU A 230 N ASP A 174
SHEET 8 AA1 8 ALA A 259 VAL A 264 1 O THR A 260 N ILE A 231
SHEET 1 AA2 2 THR A 145 SER A 148 0
SHEET 2 AA2 2 LEU A 151 ASP A 154 -1 O LEU A 151 N SER A 148
SSBOND 1 CYS A 187 CYS A 243 1555 1555 2.03
LINK OG SER A 128 S AES A 701 1555 1555 1.47
CISPEP 1 TRP A 94 PRO A 95 0 7.84
SITE 1 AC1 14 SER A 55 ALA A 56 SER A 128 SER A 129
SITE 2 AC1 14 PRO A 178 MET A 184 VAL A 188 ASN A 191
SITE 3 AC1 14 PRO A 196 GLU A 197 VAL A 239 HIS A 269
SITE 4 AC1 14 HOH A 811 HOH A 876
CRYST1 107.560 107.560 44.378 90.00 90.00 90.00 P 43 21 2 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.009297 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009297 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022534 0.00000
TER 4253 LYS A 292
MASTER 271 0 1 13 10 0 4 6 2356 1 25 23
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