HEADER HYDROLASE 13-AUG-23 8KEU TITLE CRYSTAL STRUCTURES OF ENDO-BETA-1,4-XYLANASE II MUTANT T2CT28C COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE II; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHODERMA REESEI; SOURCE 3 ORGANISM_TAXID: 51453; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENDO-BETA-1, 4-XYLANASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.LI REVDAT 1 14-AUG-24 8KEU 0 JRNL AUTH Z.LI JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF XYLANASE T2CT28C JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 78465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3966 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 17.0600 - 3.3300 1.00 2921 156 0.1517 0.1437 REMARK 3 2 3.3300 - 2.6500 1.00 2806 135 0.1395 0.1456 REMARK 3 3 2.6500 - 2.3100 1.00 2774 147 0.1410 0.1619 REMARK 3 4 2.3100 - 2.1000 1.00 2717 156 0.1268 0.1577 REMARK 3 5 2.1000 - 1.9500 1.00 2739 156 0.1192 0.1295 REMARK 3 6 1.9500 - 1.8400 1.00 2744 119 0.1180 0.1386 REMARK 3 7 1.8400 - 1.7500 1.00 2714 143 0.1144 0.1313 REMARK 3 8 1.7500 - 1.6700 1.00 2737 150 0.1086 0.1326 REMARK 3 9 1.6700 - 1.6100 1.00 2681 166 0.1065 0.1217 REMARK 3 10 1.6100 - 1.5500 1.00 2695 145 0.1024 0.1187 REMARK 3 11 1.5500 - 1.5000 1.00 2698 148 0.1081 0.1277 REMARK 3 12 1.5000 - 1.4600 1.00 2703 139 0.1101 0.1343 REMARK 3 13 1.4600 - 1.4200 1.00 2717 133 0.1153 0.1438 REMARK 3 14 1.4200 - 1.3900 1.00 2657 160 0.1228 0.1361 REMARK 3 15 1.3900 - 1.3500 1.00 2686 140 0.1240 0.1434 REMARK 3 16 1.3500 - 1.3300 1.00 2685 146 0.1315 0.1851 REMARK 3 17 1.3300 - 1.3000 1.00 2701 130 0.1361 0.1462 REMARK 3 18 1.3000 - 1.2700 0.99 2645 129 0.1401 0.1544 REMARK 3 19 1.2700 - 1.2500 0.99 2693 131 0.1480 0.1614 REMARK 3 20 1.2500 - 1.2300 0.99 2682 154 0.1513 0.1773 REMARK 3 21 1.2300 - 1.2100 0.99 2636 135 0.1585 0.1728 REMARK 3 22 1.2100 - 1.1900 0.99 2683 143 0.1672 0.2010 REMARK 3 23 1.1900 - 1.1700 0.99 2630 131 0.1737 0.2047 REMARK 3 24 1.1700 - 1.1600 0.97 2593 154 0.1854 0.2221 REMARK 3 25 1.1600 - 1.1400 0.95 2542 136 0.1951 0.2461 REMARK 3 26 1.1400 - 1.1300 0.93 2493 139 0.2139 0.2233 REMARK 3 27 1.1300 - 1.1100 0.89 2367 137 0.2302 0.2528 REMARK 3 28 1.1100 - 1.1000 0.81 2160 108 0.2501 0.2661 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) : 0.091 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.83 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 : 0.005 1612 REMARK 3 ANGLE : 1.022 2217 REMARK 3 CHIRALITY : 0.089 219 REMARK 3 PLANARITY : 0.005 290 REMARK 3 DIHEDRAL : 7.710 1141 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 8KEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 17.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12700 REMARK 200 FOR THE DATA SET : 23.8570 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) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.66100 REMARK 200 FOR SHELL : 2.000 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 (%): 47.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.2M NAI, 0.1M MES, PH REMARK 280 6, VAPOR DIFFUSION, HANGING DROP, 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 23.55950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.89100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.64900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.89100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.55950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.64900 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: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 O HOH A 411 O HOH A 421 2.07 REMARK 500 O HOH A 411 O HOH A 451 2.10 REMARK 500 O HOH A 434 O HOH A 482 2.12 REMARK 500 O HOH A 471 O HOH A 506 2.15 REMARK 500 N SER A 0 O HOH A 301 2.16 REMARK 500 O HOH A 502 O HOH A 507 2.16 REMARK 500 O HOH A 422 O HOH A 441 2.16 REMARK 500 OD1 ASN A 60 OG SER A 148 2.18 REMARK 500 O HOH A 324 O HOH A 349 2.19 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 416 O HOH A 534 3654 2.14 REMARK 500 O HOH A 335 O HOH A 507 3644 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 ASN A 56 28.90 -144.41 REMARK 500 ASP A 169 -140.76 -100.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 8KEU A 1 189 UNP B2CZF9 B2CZF9_HYPJE 8 196 SEQADV 8KEU SER A 0 UNP B2CZF9 EXPRESSION TAG SEQADV 8KEU CYS A 1 UNP B2CZF9 THR 8 ENGINEERED MUTATION SEQADV 8KEU CYS A 27 UNP B2CZF9 THR 34 ENGINEERED MUTATION SEQRES 1 A 190 SER CYS ILE GLN PRO GLY THR GLY TYR ASN ASN GLY TYR SEQRES 2 A 190 PHE TYR SER TYR TRP ASN ASP GLY HIS GLY GLY VAL THR SEQRES 3 A 190 TYR CYS ASN GLY PRO GLY GLY GLN PHE SER VAL ASN TRP SEQRES 4 A 190 SER ASN SER GLY ASN PHE VAL GLY GLY LYS GLY TRP GLN SEQRES 5 A 190 PRO GLY THR LYS ASN LYS VAL ILE ASN PHE SER GLY SER SEQRES 6 A 190 TYR ASN PRO ASN GLY ASN SER TYR LEU SER VAL TYR GLY SEQRES 7 A 190 TRP SER ARG ASN PRO LEU ILE GLU TYR TYR ILE VAL GLU SEQRES 8 A 190 ASN PHE GLY THR TYR ASN PRO SER THR GLY ALA THR LYS SEQRES 9 A 190 LEU GLY GLU VAL THR SER ASP GLY SER VAL TYR ASP ILE SEQRES 10 A 190 TYR ARG THR GLN ARG VAL ASN GLN PRO SER ILE ILE GLY SEQRES 11 A 190 THR ALA THR PHE TYR GLN TYR TRP SER VAL ARG ARG ASN SEQRES 12 A 190 HIS ARG SER SER GLY SER VAL ASN THR ALA ASN HIS PHE SEQRES 13 A 190 ASN ALA TRP ALA GLN GLN GLY LEU THR LEU GLY THR MET SEQRES 14 A 190 ASP TYR GLN ILE VAL ALA VAL GLU GLY TYR PHE SER SER SEQRES 15 A 190 GLY SER ALA SER ILE THR VAL SER HET MES A 201 12 HET MES A 202 12 HET IOD A 203 1 HET IOD A 204 1 HET IOD A 205 1 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM IOD IODIDE ION FORMUL 2 MES 2(C6 H13 N O4 S) FORMUL 4 IOD 3(I 1-) FORMUL 7 HOH *241(H2 O) HELIX 1 AA1 THR A 151 GLN A 161 1 11 SHEET 1 AA1 9 GLY A 5 ASN A 9 0 SHEET 2 AA1 9 TYR A 12 ASN A 18 -1 O TYR A 12 N ASN A 9 SHEET 3 AA1 9 ASN A 43 TRP A 50 -1 O VAL A 45 N TRP A 17 SHEET 4 AA1 9 THR A 167 TYR A 178 -1 O GLN A 171 N TRP A 50 SHEET 5 AA1 9 SER A 71 ARG A 80 -1 N TYR A 76 O ILE A 172 SHEET 6 AA1 9 ILE A 84 PHE A 92 -1 O TYR A 86 N GLY A 77 SHEET 7 AA1 9 ALA A 131 ARG A 140 1 O SER A 138 N VAL A 89 SHEET 8 AA1 9 SER A 112 GLN A 124 -1 N ARG A 121 O PHE A 133 SHEET 9 AA1 9 THR A 102 SER A 109 -1 N LEU A 104 O ILE A 116 SHEET 1 AA2 5 VAL A 24 ASN A 28 0 SHEET 2 AA2 5 GLN A 33 TRP A 38 -1 O ASN A 37 N THR A 25 SHEET 3 AA2 5 SER A 181 SER A 189 -1 O GLY A 182 N TRP A 38 SHEET 4 AA2 5 VAL A 58 ASN A 68 -1 N ASN A 68 O SER A 181 SHEET 5 AA2 5 GLY A 147 ASN A 150 -1 O VAL A 149 N ILE A 59 SSBOND 1 CYS A 1 CYS A 27 1555 1555 2.03 CISPEP 1 GLN A 51 PRO A 52 0 0.50 CISPEP 2 ASN A 81 PRO A 82 0 7.38 CRYST1 47.119 59.298 69.782 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 0.021223 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016864 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014330 0.00000