HEADER HYDROLASE 15-OCT-12 4HKL TITLE CRYSTAL STRUCTURES OF MUTANT ENDO-BETA-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, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.LANGAN,Q.WAN,L.COATES,A.KOVALEVSKY REVDAT 5 28-FEB-24 4HKL 1 REMARK REVDAT 4 24-JAN-18 4HKL 1 AUTHOR REVDAT 3 15-NOV-17 4HKL 1 REMARK REVDAT 2 12-FEB-14 4HKL 1 JRNL REVDAT 1 08-JAN-14 4HKL 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. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 81236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.120 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.129 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 4108 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 15.0094 - 3.3677 0.99 2862 148 0.1698 0.1581 REMARK 3 2 3.3677 - 2.6780 1.00 2758 138 0.1235 0.1312 REMARK 3 3 2.6780 - 2.3409 1.00 2725 142 0.1188 0.1202 REMARK 3 4 2.3409 - 2.1275 1.00 2690 155 0.1064 0.1031 REMARK 3 5 2.1275 - 1.9754 1.00 2689 152 0.0965 0.1095 REMARK 3 6 1.9754 - 1.8592 1.00 2700 116 0.0992 0.1164 REMARK 3 7 1.8592 - 1.7662 1.00 2681 142 0.0936 0.0961 REMARK 3 8 1.7662 - 1.6894 1.00 2657 154 0.0953 0.1292 REMARK 3 9 1.6894 - 1.6245 1.00 2651 153 0.0903 0.1109 REMARK 3 10 1.6245 - 1.5685 1.00 2653 144 0.0819 0.0962 REMARK 3 11 1.5685 - 1.5195 1.00 2656 149 0.0836 0.0975 REMARK 3 12 1.5195 - 1.4761 1.00 2640 137 0.0848 0.1024 REMARK 3 13 1.4761 - 1.4373 1.00 2681 138 0.0852 0.0943 REMARK 3 14 1.4373 - 1.4022 1.00 2662 144 0.0853 0.1018 REMARK 3 15 1.4022 - 1.3704 1.00 2609 150 0.0902 0.1121 REMARK 3 16 1.3704 - 1.3412 1.00 2639 133 0.0952 0.1036 REMARK 3 17 1.3412 - 1.3144 1.00 2668 153 0.0997 0.1305 REMARK 3 18 1.3144 - 1.2896 1.00 2672 113 0.1037 0.1162 REMARK 3 19 1.2896 - 1.2666 1.00 2641 137 0.1095 0.1298 REMARK 3 20 1.2666 - 1.2451 1.00 2650 139 0.1232 0.1569 REMARK 3 21 1.2451 - 1.2251 1.00 2643 146 0.1304 0.1521 REMARK 3 22 1.2251 - 1.2062 1.00 2609 133 0.1339 0.1605 REMARK 3 23 1.2062 - 1.1885 1.00 2674 136 0.1358 0.1668 REMARK 3 24 1.1885 - 1.1718 1.00 2617 147 0.1429 0.1531 REMARK 3 25 1.1718 - 1.1559 1.00 2607 141 0.1416 0.1673 REMARK 3 26 1.1559 - 1.1409 1.00 2643 151 0.1624 0.1834 REMARK 3 27 1.1409 - 1.1267 1.00 2622 132 0.1836 0.2026 REMARK 3 28 1.1267 - 1.1131 0.99 2600 154 0.2059 0.2375 REMARK 3 29 1.1131 - 1.1002 0.96 2529 131 0.2332 0.2591 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.84 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 : 0.007 1593 REMARK 3 ANGLE : 1.315 2195 REMARK 3 CHIRALITY : 0.084 221 REMARK 3 PLANARITY : 0.007 291 REMARK 3 DIHEDRAL : 12.539 558 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 4HKL 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_1000075582. 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, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81313 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.62900 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 (%): 48.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-20 % PEG 8,000, 0.2 M NAI, 0.1 M REMARK 280 MES, PH6.0 , PH 7.0, VAPOR DIFFUSION, TEMPERATURE 298K 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 24.15350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.85850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.51600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.85850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.15350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.51600 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 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 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 HG SER A 139 HD1 HIS A 155 1.28 REMARK 500 OD1 ASN A 57 O HOH A 861 2.12 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 -140.16 -101.35 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DFB RELATED DB: PDB REMARK 900 RELATED ID: 4HK8 RELATED DB: PDB REMARK 900 RELATED ID: 4HK9 RELATED DB: PDB REMARK 900 RELATED ID: 4HKO RELATED DB: PDB DBREF 4HKL A 2 190 UNP P36217 XYN2_HYPJE 34 222 SEQADV 4HKL HIS A 44 UNP P36217 ASN 76 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 HIS 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 IOD A 500 1 HET IOD A 501 1 HET IOD A 502 1 HET IOD A 503 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 4(I 1-) FORMUL 6 HOH *261(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 HIS 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 TYR A 77 O ILE A 173 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 ASN A 38 N THR A 26 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 69 O SER A 182 SHEET 5 B 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 0.06 CISPEP 2 ASN A 82 PRO A 83 0 7.45 SITE 1 AC1 2 ASN A 82 SER A 146 SITE 1 AC2 2 ARG A 119 THR A 120 SITE 1 AC3 2 MET A 169 HOH A 692 SITE 1 AC4 2 VAL A 123 GLN A 125 CRYST1 48.307 59.032 69.717 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 0.020701 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014344 0.00000