HEADER HYDROLASE 12-MAR-18 5ZH9 TITLE CRYSTAL STRUCTURES OF MUTANT ENDO-BETA-1,4-XYLANASE II (Y88F) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDO-BETA-1,4-XYLANASE II,XYLANASE 2,1,4-BETA-D-XYLAN COMPND 5 XYLANOHYDROLASE 2,ALKALINE ENDO-BETA-1,4-XYLANASE; COMPND 6 EC: 3.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYPOCREA JECORINA (STRAIN ATCC 56765 / BCRC SOURCE 3 32924 / NRRL 11460 / RUT C-30); SOURCE 4 ORGANISM_COMMON: TRICHODERMA REESEI; SOURCE 5 ORGANISM_TAXID: 1344414; SOURCE 6 STRAIN: ATCC 56765 / BCRC 32924 / NRRL 11460 / RUT C-30; SOURCE 7 GENE: XYN2, M419DRAFT_124931; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MUTANT ENDO-BETA-1, 4-XYLANASE II (Y88F), HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,Q.WAN REVDAT 2 22-NOV-23 5ZH9 1 REMARK REVDAT 1 20-MAR-19 5ZH9 0 JRNL AUTH X.ZHANG,Q.WAN JRNL TITL CRYSTAL STRUCTURES OF MUTANT ENDO-BETA-1,4-XYLANASE II JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 70852 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3587 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 39.8061 - 3.4062 0.97 2758 139 0.1792 0.1815 REMARK 3 2 3.4062 - 2.7038 0.99 2696 136 0.1447 0.1497 REMARK 3 3 2.7038 - 2.3621 1.00 2701 143 0.1423 0.1470 REMARK 3 4 2.3621 - 2.1461 1.00 2654 144 0.1293 0.1332 REMARK 3 5 2.1461 - 1.9923 1.00 2648 153 0.1238 0.1363 REMARK 3 6 1.9923 - 1.8748 0.99 2635 121 0.1253 0.1212 REMARK 3 7 1.8748 - 1.7809 0.99 2619 141 0.1257 0.1232 REMARK 3 8 1.7809 - 1.7034 1.00 2612 146 0.1263 0.1508 REMARK 3 9 1.7034 - 1.6378 1.00 2635 151 0.1238 0.1345 REMARK 3 10 1.6378 - 1.5813 1.00 2625 145 0.1254 0.1546 REMARK 3 11 1.5813 - 1.5319 1.00 2603 149 0.1204 0.1486 REMARK 3 12 1.5319 - 1.4881 1.00 2632 134 0.1224 0.1603 REMARK 3 13 1.4881 - 1.4489 1.00 2610 139 0.1249 0.1367 REMARK 3 14 1.4489 - 1.4136 0.99 2613 132 0.1263 0.1274 REMARK 3 15 1.4136 - 1.3814 1.00 2586 158 0.1311 0.1298 REMARK 3 16 1.3814 - 1.3520 1.00 2610 126 0.1282 0.1391 REMARK 3 17 1.3520 - 1.3250 1.00 2621 147 0.1250 0.1644 REMARK 3 18 1.3250 - 1.3000 1.00 2590 131 0.1238 0.1460 REMARK 3 19 1.3000 - 1.2767 1.00 2623 124 0.1274 0.1444 REMARK 3 20 1.2767 - 1.2551 1.00 2642 123 0.1223 0.1610 REMARK 3 21 1.2551 - 1.2349 1.00 2556 146 0.1262 0.1449 REMARK 3 22 1.2349 - 1.2159 1.00 2633 135 0.1259 0.1250 REMARK 3 23 1.2159 - 1.1980 0.97 2534 137 0.1236 0.1491 REMARK 3 24 1.1980 - 1.1811 0.93 2381 132 0.1272 0.1652 REMARK 3 25 1.1811 - 1.1651 0.89 2301 122 0.1363 0.1678 REMARK 3 26 1.1651 - 1.1500 0.84 2147 133 0.1483 0.1801 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.30 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 : 0.009 1596 REMARK 3 ANGLE : 1.113 2195 REMARK 3 CHIRALITY : 0.101 221 REMARK 3 PLANARITY : 0.006 294 REMARK 3 DIHEDRAL : 12.825 543 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 5ZH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 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 : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 39.782 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.03235 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.11120 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.350 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: 2DFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.2M NAI, 0.1M MES, PH REMARK 280 6.0, EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 24.16550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.02800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.66350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.02800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.16550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.66350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 7930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 143 N CA C O CB CG OD1 REMARK 480 ASN A 143 ND2 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 ASP A 170 -138.74 -99.98 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 579 DISTANCE = 5.85 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DFC RELATED DB: PDB REMARK 900 RELATED ID: 4HKW RELATED DB: PDB REMARK 900 RELATED ID: 4HKI RELATED DB: PDB REMARK 900 RELATED ID: 4HK9 RELATED DB: PDB REMARK 900 RELATED ID: 4HKO RELATED DB: PDB DBREF 5ZH9 A 2 190 UNP P36217 XYN2_HYPJR 35 223 SEQADV 5ZH9 PHE A 88 UNP P36217 TYR 121 ENGINEERED MUTATION SEQRES 1 A 189 THR ILE GLN PRO GLY THR GLY TYR ASN ASN GLY TYR PHE SEQRES 2 A 189 TYR SER TYR TRP ASN ASP GLY HIS GLY GLY VAL THR TYR SEQRES 3 A 189 THR ASN GLY PRO GLY GLY GLN PHE SER VAL ASN TRP SER SEQRES 4 A 189 ASN SER GLY ASN PHE VAL GLY GLY LYS GLY TRP GLN PRO SEQRES 5 A 189 GLY THR LYS ASN LYS VAL ILE ASN PHE SER GLY SER TYR SEQRES 6 A 189 ASN PRO ASN GLY ASN SER TYR LEU SER VAL TYR GLY TRP SEQRES 7 A 189 SER ARG ASN PRO LEU ILE GLU TYR PHE ILE VAL GLU ASN SEQRES 8 A 189 PHE GLY THR TYR ASN PRO SER THR GLY ALA THR LYS LEU SEQRES 9 A 189 GLY GLU VAL THR SER ASP GLY SER VAL TYR ASP ILE TYR SEQRES 10 A 189 ARG THR GLN ARG VAL ASN GLN PRO SER ILE ILE GLY THR SEQRES 11 A 189 ALA THR PHE TYR GLN TYR TRP SER VAL ARG ARG ASN HIS SEQRES 12 A 189 ARG SER SER GLY SER VAL ASN THR ALA ASN HIS PHE ASN SEQRES 13 A 189 ALA TRP ALA GLN GLN GLY LEU THR LEU GLY THR MET ASP SEQRES 14 A 189 TYR GLN ILE VAL ALA VAL GLU GLY TYR PHE SER SER GLY SEQRES 15 A 189 SER ALA SER ILE THR VAL SER HET IOD A 201 1 HET IOD A 202 1 HET IOD A 203 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 3(I 1-) FORMUL 5 HOH *279(H2 O) HELIX 1 AA1 THR A 152 GLN A 162 1 11 SHEET 1 AA1 9 GLY A 6 ASN A 10 0 SHEET 2 AA1 9 TYR A 13 ASN A 19 -1 O TYR A 13 N ASN A 10 SHEET 3 AA1 9 ASN A 44 TRP A 51 -1 O VAL A 46 N TRP A 18 SHEET 4 AA1 9 THR A 168 TYR A 179 -1 O GLN A 172 N TRP A 51 SHEET 5 AA1 9 SER A 72 ARG A 81 -1 N TYR A 77 O ILE A 173 SHEET 6 AA1 9 ILE A 85 PHE A 93 -1 O TYR A 87 N GLY A 78 SHEET 7 AA1 9 ALA A 132 ARG A 141 1 O SER A 139 N VAL A 90 SHEET 8 AA1 9 SER A 113 GLN A 125 -1 N ARG A 122 O PHE A 134 SHEET 9 AA1 9 THR A 103 SER A 110 -1 N LEU A 105 O ILE A 117 SHEET 1 AA2 5 VAL A 25 ASN A 29 0 SHEET 2 AA2 5 GLN A 34 TRP A 39 -1 O ASN A 38 N THR A 26 SHEET 3 AA2 5 SER A 182 SER A 190 -1 O GLY A 183 N TRP A 39 SHEET 4 AA2 5 VAL A 59 ASN A 69 -1 N ASN A 69 O SER A 182 SHEET 5 AA2 5 GLY A 148 ASN A 151 -1 O VAL A 150 N ILE A 60 CISPEP 1 GLN A 52 PRO A 53 0 1.42 CISPEP 2 ASN A 82 PRO A 83 0 7.10 SITE 1 AC1 2 ASN A 82 SER A 146 SITE 1 AC2 1 MET A 169 CRYST1 48.331 59.327 70.056 90.00 90.00 90.00 P 21 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 0.020691 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014274 0.00000