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HEADER HYDROLASE 01-MAR-17 5X88
TITLE A CRYSTAL STRUCTURE OF CUTINASES FROM MALBRANCHEA CINNAMOMEA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CUTINASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.1.1.74;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MALBRANCHEA CINNAMOMEA;
SOURCE 3 ORGANISM_TAXID: 5041;
SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS GS115;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 644223
KEYWDS CUTINASE MALBRANCHEA CINNAMOMEA LIPOIDASE MONOMER, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Z.JIANG,S.Q.YANG,X.YOU,P.HUANG,J.W.MA
REVDAT 1 31-JAN-18 5X88 0
JRNL AUTH X.DUAN,Y.LIU,X.YOU,Z.JIANG,S.YANG,S.YANG
JRNL TITL HIGH-LEVEL EXPRESSION AND CHARACTERIZATION OF A NOVEL
JRNL TITL 2 CUTINASE FROM MALBRANCHEA CINNAMOMEA SUITABLE FOR BUTYL
JRNL TITL 3 BUTYRATE PRODUCTION.
JRNL REF BIOTECHNOL BIOFUELS V. 10 223 2017
JRNL REFN ESSN 1754-6834
JRNL PMID 28932264
JRNL DOI 10.1186/S13068-017-0912-Z
REMARK 2
REMARK 2 RESOLUTION. 1.76 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX V1.11.1
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) : 1.76
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.30
REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 16775
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.172
REMARK 3 FREE R VALUE : 0.175
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : NULL
REMARK 3 SHRINKAGE RADIUS : NULL
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 15.65
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
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 5X88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-17.
REMARK 100 THE DEPOSITION ID IS D_1300003078.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-OCT-16
REMARK 200 TEMPERATURE (KELVIN) : 80
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL17U
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16910
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760
REMARK 200 RESOLUTION RANGE LOW (A) : 28.300
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : 6.800
REMARK 200 R MERGE (I) : 0.06800
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 266.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82
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: NULL
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.35
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350,POTASSIUM CHLORIDE, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 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+1/2,-Y,-Z+1/2
REMARK 290 4555 -X+1/2,-Y,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 17.20350
REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.98350
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.20350
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.98350
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 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 HOH A 207 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 421 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 SER A 1
REMARK 465 PRO A 2
REMARK 465 VAL A 3
REMARK 465 ALA A 4
REMARK 465 VAL A 5
REMARK 465 GLU A 6
REMARK 465 LYS A 7
REMARK 465 ARG A 8
REMARK 465 GLN A 9
REMARK 465 ILE A 10
REMARK 465 PHE A 11
REMARK 465 GLY A 12
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ASP A 50 CG OD1 OD2
REMARK 470 GLU A 55 CG CD OE1 OE2
REMARK 470 GLU A 92 CD OE1 OE2
REMARK 470 ILE A 175 CG1 CG2 CD1
REMARK 470 SER A 199 OG
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 O HOH A 232 O HOH A 303 1.96
REMARK 500 OD1 ASP A 192 O HOH A 201 2.08
REMARK 500 O HOH A 251 O HOH A 308 2.13
REMARK 500 O HOH A 218 O HOH A 281 2.16
REMARK 500 O HOH A 365 O HOH A 383 2.17
REMARK 500 NH2 ARG A 54 O HOH A 202 2.17
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 THR A 35 54.54 20.09
REMARK 500 THR A 43 -95.83 -101.37
REMARK 500 SER A 112 -121.25 58.01
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 418 DISTANCE = 5.95 ANGSTROMS
REMARK 525 HOH A 419 DISTANCE = 6.50 ANGSTROMS
REMARK 525 HOH A 420 DISTANCE = 6.68 ANGSTROMS
REMARK 525 HOH A 421 DISTANCE = 7.24 ANGSTROMS
DBREF 5X88 A 1 199 PDB 5X88 5X88 1 199
SEQRES 1 A 199 SER PRO VAL ALA VAL GLU LYS ARG GLN ILE PHE GLY PRO
SEQRES 2 A 199 GLY ASP ASN ASP LEU ARG ASP GLY PRO CYS LYS ASP ILE
SEQRES 3 A 199 THR PHE ILE PHE ALA ARG GLY SER THR GLU PRO GLY LEU
SEQRES 4 A 199 MET GLY ILE THR VAL GLY PRO ASP THR CYS ASP GLU LEU
SEQRES 5 A 199 ASN ARG GLU PHE ARG GLY ARG VAL ALA CYS GLN GLY VAL
SEQRES 6 A 199 GLY PRO ARG TYR GLU ALA SER LEU ALA GLY ASN PHE LEU
SEQRES 7 A 199 PRO ARG GLY THR THR GLN ALA ALA ILE ASP GLU ALA ALA
SEQRES 8 A 199 GLU LEU PHE ASN LEU ALA HIS THR LYS CYS PRO ASN THR
SEQRES 9 A 199 GLN ILE VAL GLY GLY GLY TYR SER GLN GLY ALA ALA VAL
SEQRES 10 A 199 MET HIS GLY ALA ILE PRO GLY LEU SER ASN ALA VAL LYS
SEQRES 11 A 199 ASP GLN ILE LYS GLY VAL VAL LEU TYR GLY ASP THR ARG
SEQRES 12 A 199 ASN GLU GLN ASP GLY GLY ARG ILE PRO ASN PHE PRO THR
SEQRES 13 A 199 ASP LYS THR ASN ILE ILE CYS ASN PRO GLY ASP LEU VAL
SEQRES 14 A 199 CYS ASP GLY THR LEU ILE LEU THR ALA ALA HIS PHE THR
SEQRES 15 A 199 TYR GLY THR ARG VAL ARG GLY ALA VAL ASP TRP LEU GLU
SEQRES 16 A 199 ASP ARG LEU SER
FORMUL 2 HOH *221(H2 O)
HELIX 1 AA1 ASN A 16 GLY A 21 1 6
HELIX 2 AA2 THR A 43 PHE A 56 1 14
HELIX 3 AA3 SER A 72 LEU A 78 5 7
HELIX 4 AA4 THR A 83 CYS A 101 1 19
HELIX 5 AA5 SER A 112 ILE A 122 1 11
HELIX 6 AA6 SER A 126 GLN A 132 1 7
HELIX 7 AA7 PRO A 155 ASP A 157 5 3
HELIX 8 AA8 ASP A 167 GLY A 172 5 6
HELIX 9 AA9 THR A 177 THR A 185 5 9
HELIX 10 AB1 ARG A 186 ASP A 196 1 11
SHEET 1 AA1 5 VAL A 60 GLY A 64 0
SHEET 2 AA1 5 ILE A 26 ALA A 31 1 N ILE A 26 O ALA A 61
SHEET 3 AA1 5 GLN A 105 TYR A 111 1 O VAL A 107 N ILE A 29
SHEET 4 AA1 5 ILE A 133 TYR A 139 1 O TYR A 139 N GLY A 110
SHEET 5 AA1 5 THR A 159 ILE A 162 1 O ILE A 162 N LEU A 138
SSBOND 1 CYS A 23 CYS A 101 1555 1555 2.06
SSBOND 2 CYS A 49 CYS A 62 1555 1555 2.05
CISPEP 1 GLY A 66 PRO A 67 0 8.40
CRYST1 34.407 37.815 127.967 90.00 90.00 90.00 P 21 2 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 0.029064 0.000000 0.000000 0.00000
SCALE2 0.000000 0.026445 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007815 0.00000
TER 1380 SER A 199
MASTER 276 0 0 10 5 0 0 6 1600 1 4 16
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