HEADER HYDROLASE 15-OCT-12 4HK9 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 4 29-JUL-20 4HK9 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 15-NOV-17 4HK9 1 REMARK REVDAT 2 12-FEB-14 4HK9 1 JRNL REVDAT 1 08-JAN-14 4HK9 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 23165 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1198 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 19.9730 - 3.2180 0.96 2530 137 0.1328 0.1429 REMARK 3 2 3.2180 - 2.5559 0.97 2452 127 0.1504 0.1882 REMARK 3 3 2.5559 - 2.2333 0.98 2413 148 0.1535 0.1812 REMARK 3 4 2.2333 - 2.0293 0.98 2429 132 0.1395 0.1643 REMARK 3 5 2.0293 - 1.8840 0.99 2427 126 0.1410 0.1950 REMARK 3 6 1.8840 - 1.7730 0.99 2440 131 0.1536 0.1874 REMARK 3 7 1.7730 - 1.6842 1.00 2449 128 0.1740 0.2183 REMARK 3 8 1.6842 - 1.6110 1.00 2421 139 0.1750 0.2292 REMARK 3 9 1.6110 - 1.5490 1.00 2406 130 0.1868 0.2092 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) : 15.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.72 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 1544 REMARK 3 ANGLE : 1.179 2110 REMARK 3 CHIRALITY : 0.077 214 REMARK 3 PLANARITY : 0.005 272 REMARK 3 DIHEDRAL : 13.329 512 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 4HK9 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_1000075570. 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 : 6.0 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 : 23195 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52100 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 (%): 35.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-20 % PEG 8,000, 0.2 M CACL2, 0.1 M REMARK 280 MES, PH6.0 , 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 21.19800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.05850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.05850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.19800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.78750 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, 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 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 407 O HOH A 473 2.06 REMARK 500 O HOH A 466 O HOH A 475 2.09 REMARK 500 O HOH A 507 O HOH A 549 2.13 REMARK 500 O HOH A 316 O HOH A 348 2.15 REMARK 500 O HOH A 458 O HOH A 553 2.17 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 316 O HOH A 454 4455 2.11 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 -141.63 -99.27 REMARK 500 REMARK 500 REMARK: NULL 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: 4HKL RELATED DB: PDB REMARK 900 RELATED ID: 4HKO RELATED DB: PDB DBREF 4HK9 A 3 190 UNP P36217 XYN2_HYPJE 35 222 SEQADV 4HK9 HIS A 44 UNP P36217 ASN 76 ENGINEERED MUTATION SEQRES 1 A 188 ILE GLN PRO GLY THR GLY TYR ASN ASN GLY TYR PHE TYR SEQRES 2 A 188 SER TYR TRP ASN ASP GLY HIS GLY GLY VAL THR TYR THR SEQRES 3 A 188 ASN GLY PRO GLY GLY GLN PHE SER VAL ASN TRP SER ASN SEQRES 4 A 188 SER GLY HIS PHE VAL GLY GLY LYS GLY TRP GLN PRO GLY SEQRES 5 A 188 THR LYS ASN LYS VAL ILE ASN PHE SER GLY SER TYR ASN SEQRES 6 A 188 PRO ASN GLY ASN SER TYR LEU SER VAL TYR GLY TRP SER SEQRES 7 A 188 ARG ASN PRO LEU ILE GLU TYR TYR ILE VAL GLU ASN PHE SEQRES 8 A 188 GLY THR TYR ASN PRO SER THR GLY ALA THR LYS LEU GLY SEQRES 9 A 188 GLU VAL THR SER ASP GLY SER VAL TYR ASP ILE TYR ARG SEQRES 10 A 188 THR GLN ARG VAL ASN GLN PRO SER ILE ILE GLY THR ALA SEQRES 11 A 188 THR PHE TYR GLN TYR TRP SER VAL ARG ARG ASN HIS ARG SEQRES 12 A 188 SER SER GLY SER VAL ASN THR ALA ASN HIS PHE ASN ALA SEQRES 13 A 188 TRP ALA GLN GLN GLY LEU THR LEU GLY THR MET ASP TYR SEQRES 14 A 188 GLN ILE VAL ALA VAL GLU GLY TYR PHE SER SER GLY SER SEQRES 15 A 188 ALA SER ILE THR VAL SER HET XYP B 1 10 HET XYP B 2 9 HET XYP B 3 9 HETNAM XYP BETA-D-XYLOPYRANOSE FORMUL 2 XYP 3(C5 H10 O5) FORMUL 3 HOH *256(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 15 N GLY A 8 SHEET 3 A 9 HIS A 44 TRP A 51 -1 O VAL A 46 N TRP A 18 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 ASP A 116 O VAL A 140 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 69 O SER A 182 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 1.43 LINK O4 XYP B 2 C1 XYP B 3 1555 1555 1.42 CISPEP 1 GLN A 52 PRO A 53 0 2.67 CISPEP 2 ASN A 82 PRO A 83 0 7.00 CRYST1 42.396 59.575 62.117 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 0.023587 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016099 0.00000 MASTER 255 0 3 1 14 0 0 6 0 0 0 15 END