HEADER HYDROLASE 26-MAR-18 5ZKZ TITLE CRYSTAL STRUCTURES OF MUTANT ENDO-BETA-1,4-XYLANASE II(Y77F) COMPLEXED TITLE 2 WITH 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; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYPOCREA JECORINA (STRAIN ATCC 56765 / BCRC SOURCE 3 32924 / NRRL 11460 / RUT C-30); SOURCE 4 ORGANISM_COMMON: TRICHODERMA REESEI; SOURCE 5 ORGANISM_TAXID: 1344414; SOURCE 6 STRAIN: ATCC 56765 / BCRC 32924 / NRRL 11460 / RUT C-30; SOURCE 7 GENE: XYN2, M419DRAFT_124931; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS XYLANASE II, COMPLEX, CO-CRYSTALLIZATION, XYLOTRIOSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,Q.WAN REVDAT 3 22-NOV-23 5ZKZ 1 HETSYN LINK REVDAT 2 29-JUL-20 5ZKZ 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 10-APR-19 5ZKZ 0 JRNL AUTH Q.WAN,X.ZHANG JRNL TITL CRYSTAL STRUCTURES OF ENDO-BETA-1,4-XYLANASE II JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Q.WAN,J.M.PARKS,B.L.HANSON,S.Z.FISHER,A.OSTERMANN, REMARK 1 AUTH 2 T.E.SCHRADER,D.E.GRAHAM,L.COATES,P.LANGAN,A.KOVALEVSKY REMARK 1 TITL DIRECT DETERMINATION OF PROTONATION STATES AND VISUALIZATION REMARK 1 TITL 2 OF HYDROGEN BONDING IN A GLYCOSIDE HYDROLASE WITH NEUTRON REMARK 1 TITL 3 CRYSTALLOGRAPHY. REMARK 1 REF PROC. NATL. ACAD. SCI. V. 112 12384 2015 REMARK 1 REF 2 U.S.A. REMARK 1 REFN ESSN 1091-6490 REMARK 1 PMID 26392527 REMARK 1 DOI 10.1073/PNAS.1504986112 REMARK 1 REFERENCE 2 REMARK 1 AUTH Q.WAN,Q.ZHANG,S.HAMILTON-BREHM,K.WEISS,M.MUSTYAKIMOV, REMARK 1 AUTH 2 L.COATES,P.LANGAN,D.GRAHAM,A.KOVALEVSKY REMARK 1 TITL X-RAY CRYSTALLOGRAPHIC STUDIES OF FAMILY 11 XYLANASE REMARK 1 TITL 2 MICHAELIS AND PRODUCT COMPLEXES: IMPLICATIONS FOR THE REMARK 1 TITL 3 CATALYTIC MECHANISM. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 70 11 2014 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 24419374 REMARK 1 DOI 10.1107/S1399004713023626 REMARK 2 REMARK 2 RESOLUTION. 1.30 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 50473 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) : 0.173 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2539 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 45.1104 - 3.4065 1.00 2878 141 0.1666 0.1479 REMARK 3 2 3.4065 - 2.7039 1.00 2740 153 0.1545 0.1577 REMARK 3 3 2.7039 - 2.3622 1.00 2699 147 0.1561 0.1552 REMARK 3 4 2.3622 - 2.1462 1.00 2692 147 0.1568 0.1525 REMARK 3 5 2.1462 - 1.9924 1.00 2657 141 0.1554 0.1978 REMARK 3 6 1.9924 - 1.8749 1.00 2700 119 0.1581 0.1688 REMARK 3 7 1.8749 - 1.7810 1.00 2657 154 0.1606 0.1772 REMARK 3 8 1.7810 - 1.7035 1.00 2626 150 0.1652 0.1731 REMARK 3 9 1.7035 - 1.6379 1.00 2642 137 0.1681 0.1658 REMARK 3 10 1.6379 - 1.5814 1.00 2650 151 0.1714 0.1763 REMARK 3 11 1.5814 - 1.5319 1.00 2662 129 0.2026 0.2248 REMARK 3 12 1.5319 - 1.4881 1.00 2619 152 0.2051 0.2265 REMARK 3 13 1.4881 - 1.4489 0.99 2630 120 0.2206 0.2421 REMARK 3 14 1.4489 - 1.4136 0.99 2644 143 0.2145 0.2214 REMARK 3 15 1.4136 - 1.3815 0.99 2587 157 0.2424 0.2375 REMARK 3 16 1.3815 - 1.3521 0.99 2639 128 0.2708 0.2516 REMARK 3 17 1.3521 - 1.3250 0.99 2586 140 0.2647 0.2821 REMARK 3 18 1.3250 - 1.3000 0.99 2626 130 0.3089 0.3053 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.70 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 : 0.015 1568 REMARK 3 ANGLE : 1.455 2144 REMARK 3 CHIRALITY : 0.095 219 REMARK 3 PLANARITY : 0.009 277 REMARK 3 DIHEDRAL : 13.295 519 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 5ZKZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-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 : BL17U1 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 : 50491 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.083 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.03190 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.28650 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.510 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 (%): 48.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 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 24.59750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.85450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.55450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.85450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.59750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.55450 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: 980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 O4 XYP B 1 O5 XYP B 2 2.13 REMARK 500 O4 XYP B 2 O5 XYP B 3 2.16 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 ASN A 57 26.14 -140.74 REMARK 500 ASP A 170 -137.75 -94.74 REMARK 500 REMARK 500 REMARK: NULL 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: 4HKI RELATED DB: PDB REMARK 900 RELATED ID: 4HK9 RELATED DB: PDB REMARK 900 RELATED ID: 4HKO RELATED DB: PDB DBREF 5ZKZ A 2 190 UNP P36217 XYN2_HYPJR 35 223 SEQADV 5ZKZ PHE A 77 UNP P36217 TYR 110 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 PHE 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 XYP B 1 20 HET XYP B 2 18 HET XYP B 3 18 HET GOL A 204 14 HET IOD A 205 1 HET IOD A 206 1 HET IOD A 207 1 HETNAM XYP BETA-D-XYLOPYRANOSE HETNAM GOL GLYCEROL HETNAM IOD IODIDE ION HETSYN XYP BETA-D-XYLOSE; D-XYLOSE; XYLOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 XYP 3(C5 H10 O5) FORMUL 3 GOL C3 H8 O3 FORMUL 4 IOD 3(I 1-) FORMUL 7 HOH *243(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 17 N GLY A 6 SHEET 3 AA1 9 ASN 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 PHE 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 LYS A 104 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 69 O SER A 182 SHEET 5 AA2 5 GLY A 148 ASN A 151 -1 O VAL A 150 N ILE A 60 LINK O4 XYP B 1 C1 XYP B 2 1555 1555 1.19 LINK O4 XYP B 2 C1 XYP B 3 1555 1555 1.31 CISPEP 1 GLN A 52 PRO A 53 0 13.44 CISPEP 2 ASN A 82 PRO A 83 0 10.20 CRYST1 49.195 59.109 69.709 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 0.020327 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014345 0.00000