HEADER HYDROLASE 10-MAR-18 5ZH0 TITLE CRYSTAL STRUCTURES OF ENDO-BETA-1,4-XYLANASE II 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 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 XYLANASE II, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,Q.WAN,Z.LI REVDAT 2 22-NOV-23 5ZH0 1 REMARK REVDAT 1 13-MAR-19 5ZH0 0 JRNL AUTH X.ZHANG,Q.WAN,Z.LI JRNL TITL CRYSTAL STRUCTURES OF ENDO-BETA-1,4-XYLANASE II JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.08 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 86497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 4349 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 39.8255 - 3.3552 1.00 2960 154 0.1515 0.1461 REMARK 3 2 3.3552 - 2.6633 1.00 2834 139 0.1237 0.1324 REMARK 3 3 2.6633 - 2.3266 1.00 2809 148 0.1275 0.1197 REMARK 3 4 2.3266 - 2.1139 1.00 2742 159 0.1183 0.1176 REMARK 3 5 2.1139 - 1.9624 1.00 2765 160 0.1179 0.1366 REMARK 3 6 1.9624 - 1.8467 1.00 2778 117 0.1188 0.1222 REMARK 3 7 1.8467 - 1.7542 1.00 2757 144 0.1176 0.1130 REMARK 3 8 1.7542 - 1.6779 1.00 2763 156 0.1182 0.1331 REMARK 3 9 1.6779 - 1.6133 1.00 2700 161 0.1118 0.1222 REMARK 3 10 1.6133 - 1.5576 1.00 2728 155 0.1146 0.1209 REMARK 3 11 1.5576 - 1.5089 1.00 2745 147 0.1101 0.1205 REMARK 3 12 1.5089 - 1.4658 1.00 2729 139 0.1122 0.1318 REMARK 3 13 1.4658 - 1.4272 1.00 2747 136 0.1179 0.1123 REMARK 3 14 1.4272 - 1.3924 1.00 2710 159 0.1194 0.1306 REMARK 3 15 1.3924 - 1.3607 1.00 2725 142 0.1206 0.1172 REMARK 3 16 1.3607 - 1.3317 1.00 2716 146 0.1165 0.1219 REMARK 3 17 1.3317 - 1.3051 1.00 2698 144 0.1185 0.1554 REMARK 3 18 1.3051 - 1.2805 1.00 2770 129 0.1225 0.1234 REMARK 3 19 1.2805 - 1.2576 1.00 2722 131 0.1230 0.1396 REMARK 3 20 1.2576 - 1.2363 1.00 2706 139 0.1257 0.1519 REMARK 3 21 1.2363 - 1.2163 1.00 2680 157 0.1234 0.1317 REMARK 3 22 1.2163 - 1.1976 1.00 2731 138 0.1225 0.1308 REMARK 3 23 1.1976 - 1.1800 1.00 2684 149 0.1177 0.1126 REMARK 3 24 1.1800 - 1.1634 1.00 2723 139 0.1180 0.1455 REMARK 3 25 1.1634 - 1.1477 1.00 2667 166 0.1170 0.1281 REMARK 3 26 1.1477 - 1.1328 1.00 2737 136 0.1164 0.1298 REMARK 3 27 1.1328 - 1.1186 1.00 2689 155 0.1209 0.1555 REMARK 3 28 1.1186 - 1.1051 1.00 2705 139 0.1227 0.1324 REMARK 3 29 1.1051 - 1.0923 1.00 2693 142 0.1400 0.1619 REMARK 3 30 1.0923 - 1.0800 1.00 2735 123 0.1511 0.1564 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.55 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 : 0.012 1599 REMARK 3 ANGLE : 1.622 2196 REMARK 3 CHIRALITY : 0.107 218 REMARK 3 PLANARITY : 0.009 294 REMARK 3 DIHEDRAL : 13.195 546 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 5ZH0 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_1300007056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-18 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 : BL17U1 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86497 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 39.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02949 REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27080 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 2DFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 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 24.20150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.96300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.54100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.96300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.20150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.54100 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: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 105 CD1 - CG - CD2 ANGL. DEV. = -39.5 DEGREES REMARK 500 LEU A 105 CB - CG - CD2 ANGL. DEV. = 26.0 DEGREES 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 57 27.38 -140.01 REMARK 500 ASP A 170 -141.84 -97.91 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 GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 202 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 5ZH0 A 2 190 UNP P36217 XYN2_HYPJR 35 223 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 TYR 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 GOL A 201 14 HET IOD A 202 1 HETNAM GOL GLYCEROL HETNAM IOD IODIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 IOD I 1- FORMUL 4 HOH *273(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 15 N GLY A 8 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 SER A 36 N THR A 28 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 GLY A 148 N PHE A 62 CISPEP 1 GLN A 52 PRO A 53 0 5.85 CISPEP 2 ASN A 82 PRO A 83 0 11.95 SITE 1 AC1 9 ASN A 44 GLU A 86 TYR A 88 GLU A 177 SITE 2 AC1 9 HOH A 375 HOH A 382 HOH A 400 HOH A 415 SITE 3 AC1 9 HOH A 464 SITE 1 AC2 2 ASN A 82 SER A 146 CRYST1 48.403 59.082 69.926 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 0.020660 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014301 0.00000