HEADER HYDROLASE 15-OCT-12 4HK8 TITLE CRYSTAL STRUCTURES OF MUTANT ENDO- -1,4-XYLANASE II COMPLEXED WITH TITLE 2 SUBSTRATE (1.15 A) AND PRODUCTS (1.6 A) 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; COMPND 5 EC: 3.2.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA REESEI; SOURCE 3 ORGANISM_TAXID: 51453; SOURCE 4 GENE: XYN2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJEXPRESS401 KEYWDS XYLANASE II, XYLOHEXAOSE, XYLOTRIOSE, INDUCED FIT MECHANISM, KEYWDS 2 OXOCARBENIUM ION, PALM-HAND MOTIF, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.LANGAN,Q.WAN,L.COATES,A.KOVALEVSKY REVDAT 5 28-FEB-24 4HK8 1 HETSYN LINK REVDAT 4 29-JUL-20 4HK8 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 15-NOV-17 4HK8 1 REMARK REVDAT 2 12-FEB-14 4HK8 1 JRNL REVDAT 1 08-JAN-14 4HK8 0 JRNL AUTH Q.WAN,Q.ZHANG,S.HAMILTON-BREHM,K.WEISS,M.MUSTYAKIMOV, JRNL AUTH 2 L.COATES,P.LANGAN,D.GRAHAM,A.KOVALEVSKY 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 ACTA CRYSTALLOGR.,SECT.D V. 70 11 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24419374 JRNL DOI 10.1107/S1399004713023626 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 18.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 63830 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.112 REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3239 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 18.5719 - 3.2679 0.99 3101 167 0.1434 0.1515 REMARK 3 2 3.2679 - 2.5961 0.99 2970 165 0.1187 0.1244 REMARK 3 3 2.5961 - 2.2686 0.98 2886 157 0.1116 0.1276 REMARK 3 4 2.2686 - 2.0615 0.97 2886 137 0.0937 0.1107 REMARK 3 5 2.0615 - 1.9139 0.97 2818 160 0.0913 0.1058 REMARK 3 6 1.9139 - 1.8011 0.96 2792 163 0.0909 0.1133 REMARK 3 7 1.8011 - 1.7110 0.96 2766 161 0.0904 0.1272 REMARK 3 8 1.7110 - 1.6366 0.94 2715 163 0.0897 0.1117 REMARK 3 9 1.6366 - 1.5736 0.94 2706 126 0.0859 0.1163 REMARK 3 10 1.5736 - 1.5193 0.92 2666 132 0.0852 0.0996 REMARK 3 11 1.5193 - 1.4718 0.91 2593 163 0.0886 0.1213 REMARK 3 12 1.4718 - 1.4298 0.90 2573 157 0.0927 0.1345 REMARK 3 13 1.4298 - 1.3922 0.88 2549 132 0.0947 0.1263 REMARK 3 14 1.3922 - 1.3582 0.87 2535 114 0.1001 0.1254 REMARK 3 15 1.3582 - 1.3273 0.88 2518 122 0.1036 0.1235 REMARK 3 16 1.3273 - 1.2991 0.86 2454 153 0.1084 0.1045 REMARK 3 17 1.2991 - 1.2731 0.86 2464 142 0.1133 0.1429 REMARK 3 18 1.2731 - 1.2491 0.85 2454 118 0.1163 0.1495 REMARK 3 19 1.2491 - 1.2268 0.85 2408 124 0.1285 0.1426 REMARK 3 20 1.2268 - 1.2060 0.85 2450 125 0.1288 0.1424 REMARK 3 21 1.2060 - 1.1865 0.84 2440 132 0.1371 0.1354 REMARK 3 22 1.1865 - 1.1683 0.86 2419 128 0.1502 0.1788 REMARK 3 23 1.1683 - 1.1511 0.83 2428 98 0.1550 0.1756 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) : 10.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.75 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 : 0.012 1653 REMARK 3 ANGLE : 1.479 2262 REMARK 3 CHIRALITY : 0.080 230 REMARK 3 PLANARITY : 0.007 287 REMARK 3 DIHEDRAL : 15.838 547 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 4HK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63877 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE TRIBASIC PH7.0, REMARK 280 20% PEG 3350, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 19.24600 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.70850 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 19.24600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.70850 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 424 LIES ON A SPECIAL POSITION. 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 HG SER A 139 HD1 HIS A 155 1.34 REMARK 500 HH21 ARG A 122 O HOH A 417 1.47 REMARK 500 O4 XYP B 3 O5 XYP B 4 2.18 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 -139.84 -104.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DFB RELATED DB: PDB REMARK 900 RELATED ID: 4HK9 RELATED DB: PDB REMARK 900 RELATED ID: 4HKL RELATED DB: PDB REMARK 900 RELATED ID: 4HKO RELATED DB: PDB DBREF 4HK8 A 2 190 UNP P36217 XYN2_HYPJE 34 222 SEQADV 4HK8 GLN A 177 UNP P36217 GLU 209 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 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 XYP B 1 10 HET XYP B 2 9 HET XYP B 3 9 HET XYP B 4 9 HET XYP B 5 9 HET XYP B 6 9 HET GOL A 207 6 HET GOL A 208 6 HET GOL A 209 6 HET GOL A 210 6 HET GOL A 211 6 HET CIT A 212 13 HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM GOL GLYCEROL HETNAM CIT CITRIC ACID HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 XYP 6(C5 H10 O5) FORMUL 3 GOL 5(C3 H8 O3) FORMUL 8 CIT C6 H8 O7 FORMUL 9 HOH *203(H2 O) HELIX 1 1 THR A 152 GLN A 162 1 11 SHEET 1 A 9 GLY A 6 ASN A 10 0 SHEET 2 A 9 TYR A 13 ASN A 19 -1 O TYR A 13 N ASN A 10 SHEET 3 A 9 ASN A 44 TRP A 51 -1 O GLY A 50 N PHE A 14 SHEET 4 A 9 THR A 168 TYR A 179 -1 O GLN A 172 N TRP A 51 SHEET 5 A 9 SER A 72 ARG A 81 -1 N TRP A 79 O ASP A 170 SHEET 6 A 9 ILE A 85 PHE A 93 -1 O TYR A 87 N GLY A 78 SHEET 7 A 9 ALA A 132 ARG A 141 1 O SER A 139 N VAL A 90 SHEET 8 A 9 SER A 113 GLN A 125 -1 N ARG A 122 O PHE A 134 SHEET 9 A 9 THR A 103 SER A 110 -1 N LEU A 105 O ILE A 117 SHEET 1 B 5 VAL A 25 ASN A 29 0 SHEET 2 B 5 GLN A 34 TRP A 39 -1 O SER A 36 N THR A 28 SHEET 3 B 5 SER A 182 SER A 190 -1 O GLY A 183 N TRP A 39 SHEET 4 B 5 VAL A 59 ASN A 69 -1 N ASN A 67 O SER A 184 SHEET 5 B 5 GLY A 148 ASN A 151 -1 O GLY A 148 N PHE A 62 LINK O4 XYP B 1 C1 XYP B 2 1555 1555 1.40 LINK O4 XYP B 2 C1 XYP B 3 1555 1555 1.38 LINK O4 XYP B 3 C1 XYP B 4 1555 1555 1.45 LINK O4 XYP B 4 C1 XYP B 5 1555 1555 1.40 LINK O4 XYP B 5 C1 XYP B 6 1555 1555 1.39 CISPEP 1 GLN A 52 PRO A 53 0 -6.68 CISPEP 2 ASN A 82 PRO A 83 0 5.70 CRYST1 38.492 45.526 111.417 90.00 90.00 90.00 P 21 2 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 0.025979 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008975 0.00000