HEADER HYDROLASE 13-APR-19 6JUG TITLE CRYSTAL STRUCTURES OF ENDO-BETA-1,4-XYLANASE II COMPLEXED WITH TITLE 2 XYLOTRIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: XYLANASE 2,1,4-BETA-D-XYLAN XYLANOHYDROLASE 2,ALKALINE ENDO- COMPND 5 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: TRICHODERMA REESEI RUT C-30; SOURCE 3 ORGANISM_COMMON: TRICHODERMA REESEI; SOURCE 4 ORGANISM_TAXID: 1344414; SOURCE 5 STRAIN: RUT C-30; SOURCE 6 GENE: XYN2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS XYLANASE II, COMPLEX, XYLOTRIOSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.LI,Q.WAN REVDAT 3 22-NOV-23 6JUG 1 REMARK REVDAT 2 23-DEC-20 6JUG 1 JRNL REVDAT 1 15-APR-20 6JUG 0 JRNL AUTH Z.LI,X.ZHANG,C.LI,A.KOVALEVSKY,Q.WAN JRNL TITL STUDYING THE ROLE OF A SINGLE MUTATION OF A FAMILY 11 JRNL TITL 2 GLYCOSIDE HYDROLASE USING HIGH-RESOLUTION X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF PROTEIN J. V. 39 671 2020 JRNL REFN ISSN 1572-3887 JRNL PMID 33128114 JRNL DOI 10.1007/S10930-020-09938-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.QUN,Z.QIU REMARK 1 TITL X-RAY CRYSTALLOGRAPHIC STUDIES OF FAMILY 11 XYLANASE REMARK 1 TITL 2 MICHAELIS AND PRODUCT COMPLEXES: IMPLICATIONS FOR THE REMARK 1 TITL 3 CATALYTIC MECHANISM REMARK 1 REF ACTA CRYSTALLOGRAPHICA V. D70 11 2014 REMARK 1 REF 2 SECTION D-BIOLOGICAL REMARK 1 REF 3 CRYSTALLOGRAPHY REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 24419374 REMARK 1 DOI 10.1107/S1399004713023626 REMARK 1 REFERENCE 2 REMARK 1 AUTH Q.WAN,M.P.JERRY REMARK 1 TITL DIRECT DETERMINATION OF PROTONATION STATES AND VISUALIZATION REMARK 1 TITL 2 OF HYDROGEN BONDING IN A GLYCOSIDE HYDROLASE WITH NEUTRON REMARK 1 TITL 3 CRYSTALLOGRAPHY. REMARK 1 REF PNAS V. 112 12384 2015 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 26392527 REMARK 1 DOI 10.1073/PNAS.1504986112 REMARK 2 REMARK 2 RESOLUTION. 1.19 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) : 1.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 63593 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 3204 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 37.4644 - 3.3834 0.97 2799 145 0.1594 0.1507 REMARK 3 2 3.3834 - 2.6858 0.99 2727 137 0.1331 0.1461 REMARK 3 3 2.6858 - 2.3463 0.99 2715 144 0.1327 0.1344 REMARK 3 4 2.3463 - 2.1318 0.99 2684 154 0.1227 0.1261 REMARK 3 5 2.1318 - 1.9790 0.98 2651 152 0.1154 0.1322 REMARK 3 6 1.9790 - 1.8624 0.96 2605 115 0.1165 0.1213 REMARK 3 7 1.8624 - 1.7691 0.99 2646 138 0.1188 0.1316 REMARK 3 8 1.7691 - 1.6921 0.99 2655 152 0.1222 0.1503 REMARK 3 9 1.6921 - 1.6269 0.99 2627 154 0.1206 0.1449 REMARK 3 10 1.6269 - 1.5708 0.99 2640 143 0.1229 0.1376 REMARK 3 11 1.5708 - 1.5217 0.99 2650 150 0.1258 0.1528 REMARK 3 12 1.5217 - 1.4782 0.99 2622 133 0.1262 0.1556 REMARK 3 13 1.4782 - 1.4393 0.97 2601 133 0.1330 0.1307 REMARK 3 14 1.4393 - 1.4042 0.96 2573 142 0.1338 0.1579 REMARK 3 15 1.4042 - 1.3722 0.99 2578 151 0.1400 0.1539 REMARK 3 16 1.3722 - 1.3430 0.99 2613 130 0.1387 0.1529 REMARK 3 17 1.3430 - 1.3162 0.99 2650 152 0.1381 0.1810 REMARK 3 18 1.3162 - 1.2913 0.99 2658 116 0.1414 0.1716 REMARK 3 19 1.2913 - 1.2683 0.99 2627 132 0.1378 0.1469 REMARK 3 20 1.2683 - 1.2468 1.00 2648 142 0.1465 0.1526 REMARK 3 21 1.2468 - 1.2266 0.99 2639 143 0.1475 0.1551 REMARK 3 22 1.2266 - 1.2078 0.97 2524 132 0.1522 0.1873 REMARK 3 23 1.2078 - 1.1900 0.85 2257 114 0.1590 0.1852 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.88 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 : 0.011 1566 REMARK 3 ANGLE : 1.375 2147 REMARK 3 CHIRALITY : 0.111 214 REMARK 3 PLANARITY : 0.009 286 REMARK 3 DIHEDRAL : 12.451 532 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 6JUG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-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 : 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 : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63593 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 REMARK 200 RESOLUTION RANGE LOW (A) : 37.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 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: 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 (%): 48.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, 0.2M NAI,0.1M MES, PH 6.0, REMARK 280 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 24.18950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.92550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.57000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.92550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.18950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.57000 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: 7900 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 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 -139.54 -100.15 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 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: 4HK9 RELATED DB: PDB REMARK 900 RELATED ID: 4HKI RELATED DB: PDB DBREF 6JUG A 2 190 UNP P36217 XYN2_HYPJR 35 223 SEQADV 6JUG GLU A 44 UNP P36217 ASN 77 ENGINEERED MUTATION SEQADV 6JUG GLN A 177 UNP P36217 GLU 210 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 GLU 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 GLN 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 *251(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 17 N GLY A 6 SHEET 3 AA1 9 GLU A 44 TRP A 51 -1 O GLY A 50 N PHE A 14 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 67 O SER A 184 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 0.36 CISPEP 2 ASN A 82 PRO A 83 0 7.43 SITE 1 AC1 2 ASN A 82 SER A 146 SITE 1 AC2 1 MET A 169 CRYST1 48.379 59.140 69.851 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 0.020670 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016909 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014316 0.00000