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