HEADER HYDROLASE 03-MAY-19 6JZP 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA REESEI RUT C-30; SOURCE 3 ORGANISM_TAXID: 1344414; SOURCE 4 GENE: XYN2, M419DRAFT_124931; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS XYLANASE II, COMPLEX, XYLOTRIOSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.LI,Q.WAN REVDAT 2 22-NOV-23 6JZP 1 REMARK REVDAT 1 06-MAY-20 6JZP 0 JRNL AUTH Q.WAN,Z.QIU JRNL TITL X-RAY CRYSTALLOGRAPHIC STUDIES OF FAMILY 11 XYLANASE JRNL TITL 2 MICHAELIS AND PRODUCT COMPLEXES: IMPLICATIONS FOR THE JRNL TITL 3 CATALYTIC MECHANISM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.12 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 71386 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 3623 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 39.7530 - 3.3174 0.89 2754 144 0.1553 0.1505 REMARK 3 2 3.3174 - 2.6333 0.99 2943 147 0.1227 0.1311 REMARK 3 3 2.6333 - 2.3005 1.00 2887 158 0.1218 0.1174 REMARK 3 4 2.3005 - 2.0901 1.00 2898 155 0.1126 0.1351 REMARK 3 5 2.0901 - 1.9403 0.99 2853 161 0.1080 0.1319 REMARK 3 6 1.9403 - 1.8259 0.98 2841 136 0.1111 0.1040 REMARK 3 7 1.8259 - 1.7345 1.00 2845 155 0.1076 0.1454 REMARK 3 8 1.7345 - 1.6590 1.00 2866 155 0.1121 0.1473 REMARK 3 9 1.6590 - 1.5951 1.00 2828 163 0.1057 0.1396 REMARK 3 10 1.5951 - 1.5401 1.00 2865 164 0.1071 0.1124 REMARK 3 11 1.5401 - 1.4919 1.00 2814 145 0.1059 0.1279 REMARK 3 12 1.4919 - 1.4493 1.00 2860 144 0.1129 0.1404 REMARK 3 13 1.4493 - 1.4111 0.99 2814 154 0.1189 0.1345 REMARK 3 14 1.4111 - 1.3767 0.99 1913 110 0.1338 0.1403 REMARK 3 15 1.3767 - 1.3454 0.93 718 44 0.1445 0.1978 REMARK 3 16 1.3454 - 1.3168 1.00 2821 153 0.1281 0.1547 REMARK 3 17 1.3168 - 1.2904 1.00 2866 128 0.1339 0.1681 REMARK 3 18 1.2904 - 1.2661 1.00 2812 141 0.1311 0.1685 REMARK 3 19 1.2661 - 1.2435 0.99 2829 146 0.1475 0.1652 REMARK 3 20 1.2435 - 1.2224 0.99 2809 158 0.1477 0.1442 REMARK 3 21 1.2224 - 1.2027 0.98 2781 140 0.1585 0.1720 REMARK 3 22 1.2027 - 1.1841 0.95 2687 148 0.1729 0.1827 REMARK 3 23 1.1841 - 1.1667 0.91 2526 136 0.1966 0.2247 REMARK 3 24 1.1667 - 1.1503 0.83 2313 139 0.1970 0.2332 REMARK 3 25 1.1503 - 1.1348 0.71 2029 105 0.2138 0.2726 REMARK 3 26 1.1348 - 1.1200 0.57 1591 94 0.2347 0.2507 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) : 12.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.75 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 : 0.005 1570 REMARK 3 ANGLE : 0.902 2149 REMARK 3 CHIRALITY : 0.090 213 REMARK 3 PLANARITY : 0.005 286 REMARK 3 DIHEDRAL : 12.958 533 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 6JZP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300011977. 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 39.753 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02400 REMARK 200 FOR THE DATA SET : 15.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.02400 REMARK 200 FOR SHELL : 1.680 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 (%): 49.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 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 24.11800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.09450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.75650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.09450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.11800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.75650 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: 290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 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: 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 N THR A 2 C1 GOL A 201 1.45 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 ASP A 170 -140.07 -98.87 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 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 204 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: 4HKO RELATED DB: PDB REMARK 900 RELATED ID: 4HKI RELATED DB: PDB DBREF 6JZP A 2 190 UNP P36217 XYN2_HYPJR 35 223 SEQADV 6JZP GLU A 44 UNP P36217 ASN 77 CONFLICT SEQADV 6JZP ASN A 177 UNP P36217 GLU 210 CONFLICT 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 ASN GLY TYR PHE SER SER GLY SEQRES 15 A 189 SER ALA SER ILE THR VAL SER HET GOL A 201 12 HET IOD A 202 1 HET IOD A 203 1 HET IOD A 204 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 3(I 1-) FORMUL 6 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 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 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 67 O SER A 184 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 0.50 CISPEP 2 ASN A 82 PRO A 83 0 6.91 SITE 1 AC1 6 THR A 2 THR A 26 THR A 28 IOD A 204 SITE 2 AC1 6 HOH A 301 HOH A 310 SITE 1 AC2 2 ASN A 82 SER A 146 SITE 1 AC3 2 MET A 169 GOL A 201 CRYST1 48.236 59.513 70.189 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 0.020731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014247 0.00000