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HEADER HYDROLASE 08-SEP-16 5LUJ
TITLE STRUCTURE OF CUTINASE 2 FROM THERMOBIFIDA CELLULOSILYTICA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CUTINASE 2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CUTINASE;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOBIFIDA CELLULOSILYTICA;
SOURCE 3 ORGANISM_TAXID: 144786;
SOURCE 4 GENE: CUT2;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_VARIANT: GOLD;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET26B(+)
KEYWDS CUTINASE, ALPHA/BETA HYDROLASE, POLY(ETHYLENETEREPHTHLATE) (PET),
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.HROMIC,A.LYSKOWSKI,K.GRUBER
REVDAT 1 12-JUL-17 5LUJ 0
JRNL AUTH D.RIBITSCH,A.HROMIC,S.ZITZENBACHER,B.ZARTL,C.GAMERITH,
JRNL AUTH 2 A.PELLIS,A.JUNGBAUER,A.YSKOWSKI,G.STEINKELLNER,K.GRUBER,
JRNL AUTH 3 R.TSCHELIESSNIG,E.H.ACERO,G.M.GUEBITZ
JRNL TITL SMALL CAUSE, LARGE EFFECT: STRUCTURAL CHARACTERIZATION OF
JRNL TITL 2 CUTINASES FROM THERMOBIFIDA CELLULOSILYTICA.
JRNL REF BIOTECHNOL. BIOENG. 2017
JRNL REFN ESSN 1097-0290
JRNL PMID 28671263
JRNL DOI 10.1002/BIT.26372
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???)
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) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 12953
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.186
REMARK 3 R VALUE (WORKING SET) : 0.183
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930
REMARK 3 FREE R VALUE TEST SET COUNT : 638
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 41.5243 - 3.7613 1.00 2598 136 0.1612 0.2043
REMARK 3 2 3.7613 - 2.9857 1.00 2462 133 0.1966 0.2663
REMARK 3 3 2.9857 - 2.6084 1.00 2440 109 0.2073 0.2714
REMARK 3 4 2.6084 - 2.3699 1.00 2413 134 0.1877 0.2375
REMARK 3 5 2.3699 - 2.2001 1.00 2402 126 0.1679 0.2479
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) : 0.230
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.250
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 : 0.006 2001
REMARK 3 ANGLE : 0.786 2730
REMARK 3 CHIRALITY : 0.051 300
REMARK 3 PLANARITY : 0.006 359
REMARK 3 DIHEDRAL : 9.288 1192
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 5LUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-SEP-16.
REMARK 100 THE DEPOSITION ID IS D_1200001376.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 20-JUN-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : BM30A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12953
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 43.150
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 7.800
REMARK 200 R MERGE (I) : 0.10500
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 14.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 7.50
REMARK 200 R MERGE FOR SHELL (I) : 0.23500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 7.800
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: 1JFR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.19
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE AND 30%
REMARK 280 W/V PEG MONOMETHYL ETHER 2000, VAPOR DIFFUSION, TEMPERATURE
REMARK 280 293.15K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 X,-Y,-Z
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 -X,-Y+1/2,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 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.57500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.17500
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.57500
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.17500
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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9910 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 CL CL A 301 LIES ON A SPECIAL POSITION.
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 MET A 1
REMARK 465 ARG A 246
REMARK 465 ASP A 247
REMARK 465 GLY A 248
REMARK 465 LEU A 249
REMARK 465 PHE A 250
REMARK 465 GLY A 251
REMARK 465 GLU A 252
REMARK 465 ALA A 263
REMARK 465 LEU A 264
REMARK 465 GLU A 265
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 447 O HOH A 450 3557 1.86
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 ASN A 50 -178.40 -171.26
REMARK 500 THR A 62 12.64 59.38
REMARK 500 SER A 131 -114.87 60.47
REMARK 500 THR A 154 60.66 28.60
REMARK 500 HIS A 185 -82.46 -127.71
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 CL A 301
DBREF 5LUJ A 1 262 UNP E9LVH9 E9LVH9_9ACTN 1 262
SEQADV 5LUJ ALA A 263 UNP E9LVH9 EXPRESSION TAG
SEQADV 5LUJ LEU A 264 UNP E9LVH9 EXPRESSION TAG
SEQADV 5LUJ GLU A 265 UNP E9LVH9 EXPRESSION TAG
SEQRES 1 A 265 MET ALA ASN PRO TYR GLU ARG GLY PRO ASN PRO THR ASP
SEQRES 2 A 265 ALA LEU LEU GLU ALA ARG SER GLY PRO PHE SER VAL SER
SEQRES 3 A 265 GLU GLU ARG ALA SER ARG PHE GLY ALA ASP GLY PHE GLY
SEQRES 4 A 265 GLY GLY THR ILE TYR TYR PRO ARG GLU ASN ASN THR TYR
SEQRES 5 A 265 GLY ALA VAL ALA ILE SER PRO GLY TYR THR GLY THR GLN
SEQRES 6 A 265 ALA SER VAL ALA TRP LEU GLY GLU ARG ILE ALA SER HIS
SEQRES 7 A 265 GLY PHE VAL VAL ILE THR ILE ASP THR ASN THR THR LEU
SEQRES 8 A 265 ASP GLN PRO ASP SER ARG ALA ARG GLN LEU ASN ALA ALA
SEQRES 9 A 265 LEU ASP TYR MET ILE ASN ASP ALA SER SER ALA VAL ARG
SEQRES 10 A 265 SER ARG ILE ASP SER SER ARG LEU ALA VAL MET GLY HIS
SEQRES 11 A 265 SER MET GLY GLY GLY GLY THR LEU ARG LEU ALA SER GLN
SEQRES 12 A 265 ARG PRO ASP LEU LYS ALA ALA ILE PRO LEU THR PRO TRP
SEQRES 13 A 265 HIS LEU ASN LYS ASN TRP SER SER VAL ARG VAL PRO THR
SEQRES 14 A 265 LEU ILE ILE GLY ALA ASP LEU ASP THR ILE ALA PRO VAL
SEQRES 15 A 265 LEU THR HIS ALA ARG PRO PHE TYR ASN SER LEU PRO THR
SEQRES 16 A 265 SER ILE SER LYS ALA TYR LEU GLU LEU ASP GLY ALA THR
SEQRES 17 A 265 HIS PHE ALA PRO ASN ILE PRO ASN LYS ILE ILE GLY LYS
SEQRES 18 A 265 TYR SER VAL ALA TRP LEU LYS ARG PHE VAL ASP ASN ASP
SEQRES 19 A 265 THR ARG TYR THR GLN PHE LEU CYS PRO GLY PRO ARG ASP
SEQRES 20 A 265 GLY LEU PHE GLY GLU VAL GLU GLU TYR ARG SER THR CYS
SEQRES 21 A 265 PRO PHE ALA LEU GLU
HET CL A 301 1
HETNAM CL CHLORIDE ION
FORMUL 2 CL CL 1-
FORMUL 3 HOH *50(H2 O)
HELIX 1 AA1 THR A 12 ALA A 18 1 7
HELIX 2 AA2 THR A 64 SER A 67 5 4
HELIX 3 AA3 VAL A 68 SER A 77 1 10
HELIX 4 AA4 GLN A 93 ASP A 111 1 19
HELIX 5 AA5 SER A 113 SER A 118 1 6
HELIX 6 AA6 SER A 131 ARG A 144 1 14
HELIX 7 AA7 HIS A 185 LEU A 193 1 9
HELIX 8 AA8 PHE A 210 ILE A 214 5 5
HELIX 9 AA9 ASN A 216 ASP A 232 1 17
HELIX 10 AB1 ASP A 234 ARG A 236 5 3
HELIX 11 AB2 TYR A 237 CYS A 242 1 6
SHEET 1 AA1 6 VAL A 25 ALA A 30 0
SHEET 2 AA1 6 GLY A 41 PRO A 46 -1 O ILE A 43 N GLU A 28
SHEET 3 AA1 6 PHE A 80 ILE A 85 -1 O VAL A 82 N TYR A 44
SHEET 4 AA1 6 TYR A 52 SER A 58 1 N VAL A 55 O VAL A 81
SHEET 5 AA1 6 ILE A 120 HIS A 130 1 O HIS A 130 N SER A 58
SHEET 6 AA1 6 ALA A 149 LEU A 153 1 O LEU A 153 N GLY A 129
SHEET 1 AA2 3 THR A 169 ALA A 174 0
SHEET 2 AA2 3 LYS A 199 LEU A 204 1 O LEU A 204 N GLY A 173
SHEET 3 AA2 3 GLU A 255 SER A 258 -1 O GLU A 255 N GLU A 203
SSBOND 1 CYS A 242 CYS A 260 1555 1555 2.04
CISPEP 1 CYS A 242 PRO A 243 0 0.74
CISPEP 2 CYS A 260 PRO A 261 0 10.78
SITE 1 AC1 1 ARG A 29
CRYST1 36.670 43.150 152.350 90.00 90.00 90.00 P 2 21 21 4
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 0.027270 0.000000 0.000000 0.00000
SCALE2 0.000000 0.023175 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006564 0.00000
TER 1951 PHE A 262
MASTER 269 0 1 11 9 0 1 6 2001 1 2 21
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