HEADER METAL BINDING PROTEIN 19-FEB-19 6QRV TITLE X-RAY RADIATION DOSE SERIES ON XYLOSE ISOMERASE - 2.63 MGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929; SOURCE 4 GENE: XYLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.TABERMAN,C.S.BURY,M.J.VAN DER WOERD,E.H.SNELL,E.F.GARMAN REVDAT 2 24-JAN-24 6QRV 1 REMARK LINK REVDAT 1 17-JUL-19 6QRV 0 JRNL AUTH H.TABERMAN,C.S.BURY,M.J.VAN DER WOERD,E.H.SNELL,E.F.GARMAN JRNL TITL STRUCTURAL KNOWLEDGE OR X-RAY DAMAGE? A CASE STUDY ON XYLOSE JRNL TITL 2 ISOMERASE ILLUSTRATING BOTH. JRNL REF J.SYNCHROTRON RADIAT. V. 26 931 2019 JRNL REFN ESSN 1600-5775 JRNL PMID 31274415 JRNL DOI 10.1107/S1600577519005599 REMARK 2 REMARK 2 RESOLUTION. 1.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3247: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 154455 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.105 REMARK 3 R VALUE (WORKING SET) : 0.104 REMARK 3 FREE R VALUE : 0.124 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7723 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 38.7438 - 3.6345 0.93 4832 256 0.1292 0.1583 REMARK 3 2 3.6345 - 2.8851 0.99 4974 260 0.1052 0.1257 REMARK 3 3 2.8851 - 2.5205 0.99 4991 263 0.0964 0.1178 REMARK 3 4 2.5205 - 2.2901 1.00 4938 262 0.0890 0.1123 REMARK 3 5 2.2901 - 2.1259 1.00 4945 259 0.0883 0.0968 REMARK 3 6 2.1259 - 2.0006 1.00 4942 262 0.0917 0.1024 REMARK 3 7 2.0006 - 1.9004 1.00 4949 258 0.0864 0.0977 REMARK 3 8 1.9004 - 1.8177 1.00 4899 259 0.0871 0.0971 REMARK 3 9 1.8177 - 1.7477 1.00 4921 258 0.0811 0.1015 REMARK 3 10 1.7477 - 1.6874 1.00 4916 262 0.0802 0.0951 REMARK 3 11 1.6874 - 1.6346 1.00 4915 257 0.0773 0.0959 REMARK 3 12 1.6346 - 1.5879 1.00 4912 256 0.0750 0.0945 REMARK 3 13 1.5879 - 1.5461 1.00 4918 261 0.0808 0.1080 REMARK 3 14 1.5461 - 1.5084 1.00 4857 255 0.0811 0.0980 REMARK 3 15 1.5084 - 1.4741 1.00 4934 258 0.0836 0.1047 REMARK 3 16 1.4741 - 1.4427 1.00 4891 258 0.0872 0.1137 REMARK 3 17 1.4427 - 1.4139 1.00 4924 258 0.0959 0.1284 REMARK 3 18 1.4139 - 1.3872 1.00 4837 256 0.0996 0.1210 REMARK 3 19 1.3872 - 1.3624 1.00 4908 256 0.1030 0.1360 REMARK 3 20 1.3624 - 1.3393 1.00 4880 258 0.1038 0.1299 REMARK 3 21 1.3393 - 1.3177 1.00 4921 260 0.1152 0.1347 REMARK 3 22 1.3177 - 1.2974 1.00 4884 256 0.1227 0.1401 REMARK 3 23 1.2974 - 1.2784 1.00 4885 258 0.1406 0.1636 REMARK 3 24 1.2784 - 1.2603 1.00 4880 255 0.1509 0.1772 REMARK 3 25 1.2603 - 1.2433 1.00 4844 257 0.1556 0.1670 REMARK 3 26 1.2433 - 1.2272 1.00 4864 257 0.1704 0.2114 REMARK 3 27 1.2272 - 1.2118 1.00 4897 257 0.1714 0.2042 REMARK 3 28 1.2118 - 1.1972 0.99 4847 252 0.1908 0.2044 REMARK 3 29 1.1972 - 1.1833 0.98 4768 251 0.1975 0.2128 REMARK 3 30 1.1833 - 1.1700 0.96 4659 248 0.2204 0.2193 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 3755 REMARK 3 ANGLE : 1.150 5132 REMARK 3 CHIRALITY : 0.083 511 REMARK 3 PLANARITY : 0.009 716 REMARK 3 DIHEDRAL : 15.265 1450 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 6QRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100136. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.954, 0.855 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 154466 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 38.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 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: NULL REMARK 200 STARTING MODEL: 6QRR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL, ETHYLENE GLYCOL, HEPES, REMARK 280 MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.28350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.78850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.28000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.28350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.78850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.28000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.28350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.78850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.28000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.28350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.78850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.28000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 47250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 97.57700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 102.56000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 97.57700 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 102.56000 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 603 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 933 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 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 HO2 EDO A 401 MN MN A 415 1.34 REMARK 500 HO2 EDO A 401 MG MG A 416 1.50 REMARK 500 HZ2 LYS A 183 O HOH A 539 1.59 REMARK 500 OE2 GLU A 328 O HOH A 505 1.95 REMARK 500 O HOH A 887 O HOH A 898 1.96 REMARK 500 OD2 ASP A 56 O HOH A 508 2.00 REMARK 500 O HOH A 958 O HOH A 989 2.01 REMARK 500 O HOH A 841 O HOH A 961 2.04 REMARK 500 O HOH A 794 O HOH A 824 2.09 REMARK 500 O HOH A 888 O HOH A 929 2.09 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 HH12 ARG A 23 O HOH A 615 3556 1.54 REMARK 500 O HOH A 932 O HOH A 953 7545 1.98 REMARK 500 O HOH A 534 O HOH A 936 3556 2.15 REMARK 500 O HOH A 962 O HOH A 996 4566 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 THR A 17 -75.56 -85.69 REMARK 500 PHE A 94 -25.30 -141.29 REMARK 500 GLN A 186 103.12 83.74 REMARK 500 ASN A 247 -170.83 -170.08 REMARK 500 ASN A 250 73.57 -104.18 REMARK 500 LYS A 253 -174.96 178.72 REMARK 500 TYR A 254 158.91 -46.23 REMARK 500 ALA A 343 60.21 -152.60 REMARK 500 PHE A 357 -81.58 -153.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1026 DISTANCE = 6.63 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 419 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 153 OD1 REMARK 620 2 ASP A 156 OD2 100.7 REMARK 620 3 HOH A 803 O 149.0 98.1 REMARK 620 4 HOH A 983 O 103.6 113.5 45.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 415 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 97.2 REMARK 620 3 ASP A 245 OD2 98.5 89.6 REMARK 620 4 ASP A 287 OD2 153.8 85.8 107.5 REMARK 620 5 EDO A 401 O2 86.0 175.7 92.6 90.0 REMARK 620 6 HOH A 671 O 75.3 95.6 172.4 78.5 82.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 416 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 94.4 REMARK 620 3 ASP A 245 OD2 97.5 110.5 REMARK 620 4 ASP A 287 OD2 155.9 91.1 102.4 REMARK 620 5 EDO A 401 O2 83.5 163.7 85.8 84.7 REMARK 620 6 HOH A 671 O 78.2 82.8 166.4 79.3 81.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 414 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 ASP A 255 OD2 139.8 REMARK 620 3 ASP A 257 OD1 101.4 104.1 REMARK 620 4 HOH A 574 O 98.5 104.8 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 414 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 80.5 REMARK 620 3 ASP A 255 OD1 104.4 91.4 REMARK 620 4 ASP A 255 OD2 162.1 95.5 58.0 REMARK 620 5 ASP A 257 OD1 86.6 160.8 78.0 92.5 REMARK 620 6 HOH A 574 O 104.4 114.4 143.8 93.1 82.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 414 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 539 O REMARK 620 2 HOH A 574 O 82.3 REMARK 620 3 HOH A 671 O 78.4 74.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 417 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 618 O REMARK 620 2 HOH A 649 O 88.2 REMARK 620 3 HOH A 950 O 92.6 89.6 REMARK 620 4 HOH A 967 O 90.7 93.9 175.3 REMARK 620 5 HOH A 987 O 174.2 88.5 92.2 84.8 REMARK 620 6 HOH A1018 O 95.0 176.4 88.5 87.8 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 418 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 564 O REMARK 620 2 HOH A 685 O 109.5 REMARK 620 3 HOH A 909 O 73.0 113.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPA A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 419 DBREF 6QRV A 1 388 UNP P24300 XYLA_STRRU 1 388 SEQADV 6QRV ALA A 4 UNP P24300 GLN 4 CONFLICT SEQADV 6QRV VAL A 8 UNP P24300 GLU 8 CONFLICT SEQADV 6QRV GLN A 186 UNP P24300 GLU 186 CONFLICT SEQRES 1 A 388 MET ASN TYR ALA PRO THR PRO VAL ASP ARG PHE THR PHE SEQRES 2 A 388 GLY LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE SEQRES 3 A 388 GLY ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER SEQRES 4 A 388 VAL ARG ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR SEQRES 5 A 388 PHE HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SEQRES 6 A 388 SER GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA SEQRES 7 A 388 LEU ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR SEQRES 8 A 388 ASN LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE SEQRES 9 A 388 THR ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG SEQRES 10 A 388 LYS THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY SEQRES 11 A 388 ALA GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA SEQRES 12 A 388 GLU SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP SEQRES 13 A 388 ARG MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL SEQRES 14 A 388 THR SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO SEQRES 15 A 388 LYS PRO ASN GLN PRO ARG GLY ASP ILE LEU LEU PRO THR SEQRES 16 A 388 VAL GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG SEQRES 17 A 388 PRO GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU SEQRES 18 A 388 GLN MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN SEQRES 19 A 388 ALA LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN SEQRES 20 A 388 GLY GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE SEQRES 21 A 388 GLY ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP SEQRES 22 A 388 LEU LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE SEQRES 23 A 388 ASP PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL SEQRES 24 A 388 TRP ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE SEQRES 25 A 388 LEU LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU SEQRES 26 A 388 VAL GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU SEQRES 27 A 388 ALA ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU SEQRES 28 A 388 ASP ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA SEQRES 29 A 388 ALA ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN SEQRES 30 A 388 LEU ALA MET ASP HIS LEU LEU GLY ALA ARG GLY HET EDO A 401 10 HET EDO A 402 10 HET EDO A 403 10 HET EDO A 404 10 HET EDO A 405 10 HET EDO A 406 10 HET EDO A 407 20 HET EDO A 408 10 HET EDO A 409 10 HET EDO A 410 10 HET EDO A 411 20 HET EDO A 412 10 HET IPA A 413 12 HET MN A 414 3 HET MN A 415 1 HET MG A 416 1 HET MG A 417 1 HET NA A 418 1 HET NA A 419 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM IPA ISOPROPYL ALCOHOL HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL HETSYN IPA 2-PROPANOL FORMUL 2 EDO 12(C2 H6 O2) FORMUL 14 IPA C3 H8 O FORMUL 15 MN 2(MN 2+) FORMUL 17 MG 2(MG 2+) FORMUL 19 NA 2(NA 1+) FORMUL 21 HOH *526(H2 O) HELIX 1 AA1 THR A 6 ASP A 9 5 4 HELIX 2 AA2 LEU A 15 GLY A 19 1 5 HELIX 3 AA3 ASP A 35 GLY A 47 1 13 HELIX 4 AA4 ASP A 55 ILE A 59 1 5 HELIX 5 AA5 SER A 64 GLY A 83 1 20 HELIX 6 AA6 HIS A 96 LYS A 100 5 5 HELIX 7 AA7 ASP A 108 LEU A 129 1 22 HELIX 8 AA8 ASP A 150 GLY A 173 1 24 HELIX 9 AA9 THR A 195 GLU A 204 1 10 HELIX 10 AB1 ARG A 208 GLU A 210 5 3 HELIX 11 AB2 GLU A 217 MET A 223 1 7 HELIX 12 AB3 ASN A 227 ALA A 238 1 12 HELIX 13 AB4 ASP A 264 GLY A 279 1 16 HELIX 14 AB5 ASP A 295 ASP A 323 1 29 HELIX 15 AB6 ASP A 323 SER A 333 1 11 HELIX 16 AB7 ARG A 334 ALA A 339 1 6 HELIX 17 AB8 GLY A 346 ASP A 353 1 8 HELIX 18 AB9 ARG A 354 PHE A 357 5 4 HELIX 19 AC1 ASP A 361 ARG A 368 1 8 HELIX 20 AC2 ALA A 371 GLY A 385 1 15 SHEET 1 AA1 8 TYR A 212 VAL A 214 0 SHEET 2 AA1 8 ARG A 177 ILE A 180 1 N ILE A 180 O GLY A 213 SHEET 3 AA1 8 THR A 133 ALA A 136 1 N TYR A 134 O ARG A 177 SHEET 4 AA1 8 LYS A 85 THR A 90 1 N ALA A 89 O VAL A 135 SHEET 5 AA1 8 GLY A 50 HIS A 54 1 N VAL A 51 O LYS A 85 SHEET 6 AA1 8 PHE A 11 GLY A 14 1 N PHE A 13 O THR A 52 SHEET 7 AA1 8 ARG A 284 PHE A 286 1 O PHE A 286 N THR A 12 SHEET 8 AA1 8 ASP A 245 LEU A 246 1 N LEU A 246 O HIS A 285 SHEET 1 AA2 2 GLY A 142 ALA A 143 0 SHEET 2 AA2 2 ASP A 190 ILE A 191 -1 O ASP A 190 N ALA A 143 LINK OD1 ASP A 153 NA NA A 419 1555 1555 2.84 LINK OD2 ASP A 156 NA NA A 419 1555 1555 2.74 LINK OE2 GLU A 181 MN A MN A 415 1555 1555 2.08 LINK OE2 GLU A 181 MG B MG A 416 1555 1555 2.01 LINK OE2AGLU A 217 MN A MN A 414 1555 1555 2.11 LINK OE2BGLU A 217 MN B MN A 414 1555 1555 2.00 LINK OE1AGLU A 217 MN A MN A 415 1555 1555 1.81 LINK OE1BGLU A 217 MG B MG A 416 1555 1555 2.03 LINK NE2BHIS A 220 MN B MN A 414 1555 1555 2.22 LINK OD2 ASP A 245 MN A MN A 415 1555 1555 1.95 LINK OD2 ASP A 245 MG B MG A 416 1555 1555 2.04 LINK OD1BASP A 255 MN B MN A 414 1555 1555 2.24 LINK OD2AASP A 255 MN A MN A 414 1555 1555 1.89 LINK OD2BASP A 255 MN B MN A 414 1555 1555 2.26 LINK OD1AASP A 257 MN A MN A 414 1555 1555 1.89 LINK OD1BASP A 257 MN B MN A 414 1555 1555 2.35 LINK OD2 ASP A 287 MN A MN A 415 1555 1555 2.04 LINK OD2 ASP A 287 MG B MG A 416 1555 1555 2.08 LINK O2 EDO A 401 MN A MN A 415 1555 1555 2.14 LINK O2 EDO A 401 MG B MG A 416 1555 1555 2.30 LINK MN C MN A 414 O HOH A 539 1555 1555 2.78 LINK MN A MN A 414 O HOH A 574 1555 1555 1.91 LINK MN B MN A 414 O HOH A 574 1555 1555 2.25 LINK MN C MN A 414 O HOH A 574 1555 1555 1.99 LINK MN C MN A 414 O HOH A 671 1555 1555 2.61 LINK MN A MN A 415 O HOH A 671 1555 1555 2.41 LINK MG B MG A 416 O HOH A 671 1555 1555 2.34 LINK MG MG A 417 O HOH A 618 1555 1555 2.01 LINK MG MG A 417 O HOH A 649 1555 1555 2.15 LINK MG MG A 417 O HOH A 950 1555 6555 2.02 LINK MG MG A 417 O HOH A 967 1555 1555 2.05 LINK MG MG A 417 O HOH A 987 1555 1555 2.07 LINK MG MG A 417 O HOH A1018 1555 6555 1.97 LINK NA NA A 418 O HOH A 564 1555 1555 2.85 LINK NA NA A 418 O HOH A 685 1555 1555 2.66 LINK NA NA A 418 O HOH A 909 1555 1555 2.89 LINK NA NA A 419 O HOH A 803 1555 1555 3.15 LINK NA NA A 419 O HOH A 983 1555 1555 2.60 CISPEP 1 GLN A 186 PRO A 187 0 21.00 SITE 1 AC1 10 HIS A 54 TRP A 137 GLU A 181 ASP A 245 SITE 2 AC1 10 ASP A 287 MN A 415 MG A 416 HOH A 625 SITE 3 AC1 10 HOH A 671 HOH A 709 SITE 1 AC2 7 PRO A 97 VAL A 98 LYS A 100 ASP A 108 SITE 2 AC2 7 ALA A 365 ARG A 368 MET A 370 SITE 1 AC3 8 TYR A 254 GLN A 256 HOH A 514 HOH A 571 SITE 2 AC3 8 HOH A 575 HOH A 579 HOH A 830 HOH A 900 SITE 1 AC4 6 LEU A 258 ARG A 259 PRO A 291 GLU A 373 SITE 2 AC4 6 ASP A 376 HOH A 781 SITE 1 AC5 5 LYS A 159 ARG A 205 TRP A 237 HOH A 680 SITE 2 AC5 5 HOH A 690 SITE 1 AC6 5 ASP A 153 ASP A 156 HOH A 667 HOH A 774 SITE 2 AC6 5 HOH A 854 SITE 1 AC7 8 GLY A 146 GLY A 147 LYS A 149 ASP A 150 SITE 2 AC7 8 ARG A 321 LEU A 330 HOH A 524 HOH A 664 SITE 1 AC8 5 ASN A 250 GLY A 263 ASP A 264 HOH A 544 SITE 2 AC8 5 HOH A 933 SITE 1 AC9 7 TRP A 16 PHE A 26 LYS A 289 HOH A 552 SITE 2 AC9 7 HOH A 557 HOH A 631 HOH A 727 SITE 1 AD1 7 ARG A 117 LEU A 351 ASP A 352 ASP A 353 SITE 2 AD1 7 ARG A 354 GLU A 358 HOH A 542 SITE 1 AD2 7 LEU A 236 ALA A 278 GLY A 279 TYR A 280 SITE 2 AD2 7 SER A 281 HOH A 564 HOH A 988 SITE 1 AD3 11 LEU A 93 GLY A 103 PHE A 104 ALA A 136 SITE 2 AD3 11 GLY A 138 GLU A 141 HOH A 501 HOH A 512 SITE 3 AD3 11 HOH A 537 HOH A 778 HOH A 792 SITE 1 AD4 4 ASP A 361 HOH A 556 HOH A 770 HOH A 970 SITE 1 AD5 8 GLU A 217 HIS A 220 ASN A 247 ASP A 255 SITE 2 AD5 8 ASP A 257 HOH A 539 HOH A 574 HOH A 671 SITE 1 AD6 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AD6 6 EDO A 401 HOH A 671 SITE 1 AD7 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AD7 6 EDO A 401 HOH A 671 SITE 1 AD8 6 HOH A 618 HOH A 649 HOH A 950 HOH A 967 SITE 2 AD8 6 HOH A 987 HOH A1018 SITE 1 AD9 6 GLY A 239 LYS A 240 LEU A 241 HOH A 564 SITE 2 AD9 6 HOH A 685 HOH A 909 SITE 1 AE1 5 ASP A 153 ASP A 156 ARG A 157 ALA A 339 SITE 2 AE1 5 HOH A 983 CRYST1 92.567 97.577 102.560 90.00 90.00 90.00 I 2 2 2 8 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 0.010803 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010248 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009750 0.00000