HEADER HYDROLASE 20-JUL-25 9VXQ TITLE CRYSTAL STRUCTURE OF ENDO-1,4-BETA-XYLANASE FROM HYPOCREA VIRENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA VIRENS; SOURCE 3 ORGANISM_TAXID: 29875; SOURCE 4 GENE: TRIVIDRAFT_72838; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS XYLANASE, GH11, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.H.NAM REVDAT 1 22-JUL-26 9VXQ 0 JRNL AUTH K.H.NAM JRNL TITL CRYSTAL STRUCTURE OF ENDO-1,4-BETA-XYLANASE FROM HYPOCREA JRNL TITL 2 VIRENS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 15462 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1546 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 45.0600 - 4.3400 0.97 1359 150 0.1775 0.2171 REMARK 3 2 4.3400 - 3.4400 0.98 1315 146 0.1635 0.1790 REMARK 3 3 3.4400 - 3.0100 0.99 1302 145 0.1608 0.1910 REMARK 3 4 3.0100 - 2.7300 0.96 1247 139 0.1639 0.1900 REMARK 3 5 2.7300 - 2.5400 0.98 1268 140 0.1678 0.2004 REMARK 3 6 2.5400 - 2.3900 0.98 1259 140 0.1724 0.2086 REMARK 3 7 2.3900 - 2.2700 0.97 1254 140 0.1653 0.2019 REMARK 3 8 2.2700 - 2.1700 0.95 1212 134 0.1651 0.2048 REMARK 3 9 2.1700 - 2.0800 0.96 1221 136 0.1784 0.2057 REMARK 3 10 2.0800 - 2.0100 0.97 1260 140 0.1883 0.2498 REMARK 3 11 2.0100 - 1.9500 0.96 1219 136 0.1915 0.2311 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.006 1493 REMARK 3 ANGLE : 0.846 2037 REMARK 3 CHIRALITY : 0.062 202 REMARK 3 PLANARITY : 0.006 266 REMARK 3 DIHEDRAL : 7.584 211 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 9VXQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061791. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 45.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, PEG4000, NACL, SMALL TUBES, REMARK 280 TEMPERATURE 293K 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 21.66650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.22150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.63900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.22150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.66650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.63900 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 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 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 ALA A 20 REMARK 465 PRO A 21 REMARK 465 THR A 22 REMARK 465 GLU A 23 REMARK 465 SER A 24 REMARK 465 VAL A 25 REMARK 465 GLU A 26 REMARK 465 VAL A 27 REMARK 465 GLU A 28 REMARK 465 LYS A 29 REMARK 465 ARG A 30 REMARK 465 GLN A 31 REMARK 465 THR A 32 REMARK 465 ILE A 33 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 368 O HOH A 415 1.81 REMARK 500 O HOH A 384 O HOH A 416 2.07 REMARK 500 O HOH A 350 O HOH A 406 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 309 O HOH A 310 3555 1.90 REMARK 500 O HOH A 310 O HOH A 419 3545 1.93 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 200 -141.40 -93.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 9VXQ A 20 220 UNP G9MJY8 G9MJY8_HYPVG 20 220 SEQRES 1 A 201 ALA PRO THR GLU SER VAL GLU VAL GLU LYS ARG GLN THR SEQRES 2 A 201 ILE GLY PRO GLY THR GLY TYR ASN ASN GLY TYR TYR TYR SEQRES 3 A 201 SER TYR TRP ASN ASP GLY HIS SER GLY VAL THR TYR THR SEQRES 4 A 201 ASN GLY GLY GLY GLY SER PHE THR VAL ASN TRP SER ASN SEQRES 5 A 201 SER GLY ASN PHE VAL GLY GLY LYS GLY TRP GLN PRO GLY SEQRES 6 A 201 THR LYS ASN LYS VAL ILE ASN PHE SER GLY SER TYR ASN SEQRES 7 A 201 PRO ASN GLY ASN SER TYR LEU SER ILE TYR GLY TRP SER SEQRES 8 A 201 ARG ASN PRO LEU ILE GLU TYR TYR ILE VAL GLU ASN PHE SEQRES 9 A 201 GLY THR TYR ASN PRO SER THR GLY ALA THR LYS LEU GLY SEQRES 10 A 201 GLU VAL THR SER ASP GLY SER VAL TYR ASP ILE TYR ARG SEQRES 11 A 201 THR GLN ARG VAL ASN GLN PRO SER ILE ILE GLY THR ALA SEQRES 12 A 201 THR PHE TYR GLN TYR TRP SER VAL ARG ARG SER HIS ARG SEQRES 13 A 201 SER SER GLY SER VAL ASN THR ALA ASN HIS PHE ASN ALA SEQRES 14 A 201 TRP ALA SER HIS GLY LEU THR LEU GLY THR MET ASP TYR SEQRES 15 A 201 GLN ILE VAL ALA VAL GLU GLY TYR PHE SER SER GLY SER SEQRES 16 A 201 ALA SER ILE THR VAL SER FORMUL 2 HOH *132(H2 O) HELIX 1 AA1 THR A 182 HIS A 192 1 11 SHEET 1 AA1 9 GLY A 36 ASN A 40 0 SHEET 2 AA1 9 TYR A 43 ASN A 49 -1 O TYR A 43 N ASN A 40 SHEET 3 AA1 9 ASN A 74 TRP A 81 -1 O VAL A 76 N TRP A 48 SHEET 4 AA1 9 THR A 198 TYR A 209 -1 O GLN A 202 N TRP A 81 SHEET 5 AA1 9 SER A 102 ARG A 111 -1 N SER A 105 O ALA A 205 SHEET 6 AA1 9 ILE A 115 PHE A 123 -1 O ILE A 119 N ILE A 106 SHEET 7 AA1 9 ALA A 162 ARG A 171 1 O SER A 169 N VAL A 120 SHEET 8 AA1 9 SER A 143 GLN A 155 -1 N ARG A 152 O PHE A 164 SHEET 9 AA1 9 THR A 133 SER A 140 -1 N LEU A 135 O ILE A 147 SHEET 1 AA2 5 VAL A 55 ASN A 59 0 SHEET 2 AA2 5 SER A 64 TRP A 69 -1 O ASN A 68 N THR A 56 SHEET 3 AA2 5 SER A 212 SER A 220 -1 O ILE A 217 N PHE A 65 SHEET 4 AA2 5 VAL A 89 ASN A 99 -1 N ASN A 99 O SER A 212 SHEET 5 AA2 5 GLY A 178 ASN A 181 -1 O VAL A 180 N ILE A 90 CISPEP 1 GLN A 82 PRO A 83 0 2.14 CISPEP 2 ASN A 112 PRO A 113 0 6.55 CRYST1 43.333 51.278 94.443 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 0.023077 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010588 0.00000 MASTER 268 0 0 1 14 0 0 6 1579 1 0 16 END