HEADER ISOMERASE 14-MAY-14 4QDW TITLE JOINT X-RAY AND NEUTRON STRUCTURE OF STREPTOMYCES RUBIGINOSUS D-XYLOSE TITLE 2 ISOMERASE IN COMPLEX WITH TWO NI2+ IONS AND LINEAR L-ARABINOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929 KEYWDS TIM BARREL, SUGAR ISOMERASE, MONOSACCHARIDES, ISOMERASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR A.Y.KOVALEVSKY,P.LANGAN REVDAT 6 28-FEB-24 4QDW 1 REMARK LINK REVDAT 5 01-JUL-20 4QDW 1 LINK ATOM REVDAT 4 22-NOV-17 4QDW 1 REMARK REVDAT 3 24-SEP-14 4QDW 1 TITLE REVDAT 2 10-SEP-14 4QDW 1 JRNL REVDAT 1 03-SEP-14 4QDW 0 JRNL AUTH P.LANGAN,A.K.SANGHA,T.WYMORE,J.M.PARKS,Z.K.YANG,B.L.HANSON, JRNL AUTH 2 Z.FISHER,S.A.MASON,M.P.BLAKELEY,V.T.FORSYTH,J.P.GLUSKER, JRNL AUTH 3 H.L.CARRELL,J.C.SMITH,D.A.KEEN,D.E.GRAHAM,A.KOVALEVSKY JRNL TITL L-ARABINOSE BINDING, ISOMERIZATION, AND EPIMERIZATION BY JRNL TITL 2 D-XYLOSE ISOMERASE: X-RAY/NEUTRON CRYSTALLOGRAPHIC AND JRNL TITL 3 MOLECULAR SIMULATION STUDY. JRNL REF STRUCTURE V. 22 1287 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 25132082 JRNL DOI 10.1016/J.STR.2014.07.002 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NCNS 1.0.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,MUSTYAKIMOV, REMARK 3 : AFONINE,LANGAN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 28443 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1446 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6325 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 340 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3054 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC VARIMAX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL3000 FOR X-RAY AND RETREAT REMARK 200 FOR NEUTRON REMARK 200 DATA SCALING SOFTWARE : HKL3000 FOR X-RAY AND RETREAT REMARK 200 FOR NEUTRON REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64130 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 34.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.38300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 30-AUG-11 REMARK 230 TEMPERATURE (KELVIN) : 291.0 REMARK 230 PH : 7.70 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : D19 REMARK 230 WAVELENGTH OR RANGE (A) : 2.422 REMARK 230 MONOCHROMATOR : GRAPHITE REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : AREA DETECTOR REMARK 230 DETECTOR MANUFACTURER : 3HE POSITION SENSITIVE DETECTOR REMARK 230 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 FOR X-RAY, RETREAT FOR REMARK 230 NEUTRON REMARK 230 DATA SCALING SOFTWARE : D*TREK, HKL-3000 FOR X-RAY, REMARK 230 RETREAT FOR NEUTRON REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 36814 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 230 RESOLUTION RANGE LOW (A) : 71.600 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 81.5 REMARK 230 DATA REDUNDANCY : 2.700 REMARK 230 R MERGE (I) : 0.12000 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 10.5000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 230 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 230 DATA REDUNDANCY IN SHELL : 1.90 REMARK 230 R MERGE FOR SHELL (I) : 0.49000 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 1.500 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : CNS REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% AMMONIUM SULFATE, 0.1 M HEPES PH REMARK 280 7.7, BATCH, TEMPERATURE 291K 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 47.09500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.83500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.47000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.09500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.83500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.47000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.09500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.83500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.47000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.09500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.83500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.47000 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: 32620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -300.0 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 0.00000 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 -102.94000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -102.94000 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 O DOD A1129 LIES ON A SPECIAL POSITION. REMARK 375 O DOD A1194 LIES ON A SPECIAL POSITION. 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 DOD A 1059 D1 DOD A 1169 1.48 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 -74.69 -81.36 REMARK 500 ASP A 175 77.88 -106.26 REMARK 500 GLU A 186 100.51 74.82 REMARK 500 ASN A 247 -167.32 -168.99 REMARK 500 ASN A 250 79.19 -100.29 REMARK 500 LYS A 253 -166.56 -172.21 REMARK 500 PHE A 357 -67.15 -155.89 REMARK 500 REMARK 500 REMARK: NULL 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 NI A 403 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 96.7 REMARK 620 3 ASP A 245 OD2 95.4 100.2 REMARK 620 4 ASP A 287 OD2 164.6 90.9 96.4 REMARK 620 5 LAI A 404 O4 89.9 163.9 93.7 79.5 REMARK 620 6 LAI A 404 O2 77.2 91.4 166.9 89.3 75.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 79.4 REMARK 620 3 LAI A 404 O2 122.6 105.0 REMARK 620 4 LAI A 404 O1 166.0 96.0 71.3 REMARK 620 5 DOD A1001 O 92.4 165.2 89.7 89.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 73.3 REMARK 620 3 ASP A 255 OD2 177.8 106.5 REMARK 620 4 ASP A 255 OD1 118.2 103.5 59.7 REMARK 620 5 ASP A 257 OD1 94.6 167.0 85.5 77.8 REMARK 620 6 DOD A1001 O 84.7 100.3 97.4 150.8 82.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LAI A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QDP RELATED DB: PDB REMARK 900 RELATED ID: 4QE1 RELATED DB: PDB REMARK 900 RELATED ID: 4QE4 RELATED DB: PDB REMARK 900 RELATED ID: 4QE5 RELATED DB: PDB REMARK 900 RELATED ID: 4QEE RELATED DB: PDB REMARK 900 RELATED ID: 4QEH RELATED DB: PDB DBREF 4QDW A 1 388 UNP P24300 XYLA_STRRU 1 388 SEQRES 1 A 388 MET ASN TYR GLN PRO THR PRO GLU 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 GLU 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 NI A 401 1 HET NI A 402 1 HET NI A 403 1 HET LAI A 404 19 HETNAM NI NICKEL (II) ION HETNAM LAI L-ARABINOSE FORMUL 2 NI 3(NI 2+) FORMUL 5 LAI C5 H10 O5 FORMUL 6 DOD *259(D2 O) HELIX 1 1 THR A 6 ASP A 9 5 4 HELIX 2 2 LEU A 15 GLY A 19 1 5 HELIX 3 3 ASP A 35 GLY A 47 1 13 HELIX 4 4 ASP A 55 ILE A 59 1 5 HELIX 5 5 SER A 64 GLY A 83 1 20 HELIX 6 6 HIS A 96 LYS A 100 5 5 HELIX 7 7 ASP A 108 GLY A 130 1 23 HELIX 8 8 ASP A 150 GLY A 173 1 24 HELIX 9 9 THR A 195 GLU A 204 1 10 HELIX 10 10 ARG A 208 GLU A 210 5 3 HELIX 11 11 GLU A 217 MET A 223 1 7 HELIX 12 12 ASN A 227 ALA A 238 1 12 HELIX 13 13 ASP A 264 GLY A 279 1 16 HELIX 14 14 ASP A 295 ASP A 323 1 29 HELIX 15 15 ASP A 323 SER A 333 1 11 HELIX 16 16 ARG A 334 ALA A 339 1 6 HELIX 17 17 GLY A 346 ASP A 353 1 8 HELIX 18 18 ARG A 354 PHE A 357 5 4 HELIX 19 19 ASP A 361 ARG A 368 1 8 HELIX 20 20 ALA A 371 GLY A 385 1 15 SHEET 1 A 8 TYR A 212 VAL A 214 0 SHEET 2 A 8 ARG A 177 ILE A 180 1 N ILE A 180 O GLY A 213 SHEET 3 A 8 THR A 133 ALA A 136 1 N TYR A 134 O ARG A 177 SHEET 4 A 8 MET A 88 THR A 90 1 N ALA A 89 O VAL A 135 SHEET 5 A 8 GLY A 50 HIS A 54 1 N PHE A 53 O THR A 90 SHEET 6 A 8 PHE A 11 GLY A 14 1 N PHE A 13 O THR A 52 SHEET 7 A 8 ARG A 284 PHE A 286 1 O PHE A 286 N THR A 12 SHEET 8 A 8 ASP A 245 LEU A 246 1 N LEU A 246 O HIS A 285 SHEET 1 B 2 GLY A 142 ALA A 143 0 SHEET 2 B 2 ASP A 190 ILE A 191 -1 O ASP A 190 N ALA A 143 LINK OE2 GLU A 181 NI NI A 403 1555 1555 2.05 LINK OE2 GLU A 217 NI NI A 401 1555 1555 2.36 LINK OE2 GLU A 217 NI NI A 402 1555 1555 2.06 LINK OE1 GLU A 217 NI NI A 403 1555 1555 2.07 LINK NE2 HIS A 220 NI NI A 401 1555 1555 2.03 LINK NE2 HIS A 220 NI NI A 402 1555 1555 2.61 LINK OD2 ASP A 245 NI NI A 403 1555 1555 2.18 LINK OD2 ASP A 255 NI NI A 402 1555 1555 2.06 LINK OD1 ASP A 255 NI NI A 402 1555 1555 2.34 LINK OD1 ASP A 257 NI NI A 402 1555 1555 2.25 LINK OD2 ASP A 287 NI NI A 403 1555 1555 2.08 LINK NI NI A 401 O2 LAI A 404 1555 1555 2.38 LINK NI NI A 401 O1 LAI A 404 1555 1555 2.44 LINK NI NI A 401 O DOD A1001 1555 1555 1.98 LINK NI NI A 402 O DOD A1001 1555 1555 2.57 LINK NI NI A 403 O4 LAI A 404 1555 1555 2.22 LINK NI NI A 403 O2 LAI A 404 1555 1555 2.32 CISPEP 1 GLU A 186 PRO A 187 0 27.29 SITE 1 AC1 7 GLU A 217 HIS A 220 ASP A 255 NI A 402 SITE 2 AC1 7 NI A 403 LAI A 404 DOD A1001 SITE 1 AC2 7 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC2 7 NI A 401 LAI A 404 DOD A1001 SITE 1 AC3 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AC3 6 NI A 401 LAI A 404 SITE 1 AC4 17 TRP A 16 PHE A 26 HIS A 54 TRP A 137 SITE 2 AC4 17 GLU A 181 LYS A 183 GLU A 217 HIS A 220 SITE 3 AC4 17 ASP A 245 ASP A 255 ASP A 287 NI A 401 SITE 4 AC4 17 NI A 402 NI A 403 DOD A1001 DOD A1062 SITE 5 AC4 17 DOD A1096 CRYST1 94.190 99.670 102.940 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 0.010617 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009714 0.00000