HEADER ISOMERASE 20-OCT-09 3KBW TITLE ROOM TEMPERATURE X-RAY MIXED-METAL STRUCTURE OF D-XYLOSE ISOMERASE IN TITLE 2 COMPLEX WITH NI(2+) AND MG(2+) CO-FACTORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.5; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929; SOURCE 4 GENE: XYLA KEYWDS XYLOSE ISOMERASE, CARBOHYDRATE METABOLISM, METAL-BINDING, PENTOSE KEYWDS 2 SHUNT, XYLOSE METABOLISM, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.Y.KOVALEVSKY,L.HANSON,P.LANGAN REVDAT 3 21-FEB-24 3KBW 1 REMARK LINK REVDAT 2 07-MAR-12 3KBW 1 JRNL VERSN REVDAT 1 16-JUN-10 3KBW 0 JRNL AUTH A.Y.KOVALEVSKY,L.HANSON,S.Z.FISHER,M.MUSTYAKIMOV,S.A.MASON, JRNL AUTH 2 V.T.FORSYTH,M.P.BLAKELEY,D.A.KEEN,T.WAGNER,H.L.CARRELL, JRNL AUTH 3 A.K.KATZ,J.P.GLUSKER,P.LANGAN JRNL TITL METAL ION ROLES AND THE MOVEMENT OF HYDROGEN DURING REACTION JRNL TITL 2 CATALYZED BY D-XYLOSE ISOMERASE: A JOINT X-RAY AND NEUTRON JRNL TITL 3 DIFFRACTION STUDY. JRNL REF STRUCTURE V. 18 688 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20541506 JRNL DOI 10.1016/J.STR.2010.03.011 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.122 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.119 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3131 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 62867 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.109 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.106 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2506 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 50014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3053 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 312 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3338.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 3 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 30463 REMARK 3 NUMBER OF RESTRAINTS : 37750 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.023 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.047 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.063 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.015 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.061 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.114 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KBW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 293 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50014 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 (%) : 95.0 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: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40MG/ML PROTEIN, 2MM NICL2, 2MM MGCL2, REMARK 280 30% (V/V) AMMONIUM SULFATE (SAT.), PH 7.7, BATCH, TEMPERATURE REMARK 280 290K 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 46.98600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.85050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.42750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.98600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.85050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.42750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.98600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.85050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.42750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.98600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.85050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.42750 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: 30690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 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 -102.85500 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 -102.85500 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 A1127 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1149 LIES ON A SPECIAL POSITION. REMARK 450 REMARK 450 SOURCE REMARK 450 THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 24 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 32 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 32 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 42 CD - NE - CZ ANGL. DEV. = 11.8 DEGREES REMARK 500 ASP A 55 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 74 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 76 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 109 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 124 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 152 CD - NE - CZ ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 157 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 GLU A 204 OE1 - CD - OE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 TYR A 212 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 TYR A 212 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 259 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 259 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 266 CD - NE - CZ ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 266 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 308 NE - CZ - NH1 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 316 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 331 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 340 CD - NE - CZ ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 368 CD - NE - CZ ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 387 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES 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 TYR A 3 54.64 -144.17 REMARK 500 THR A 17 -75.07 -86.09 REMARK 500 PHE A 94 -23.60 -140.86 REMARK 500 GLU A 186 109.29 79.33 REMARK 500 ASN A 247 -165.15 -167.99 REMARK 500 LYS A 253 -169.65 -167.55 REMARK 500 PHE A 357 -68.56 -156.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 2 TYR A 3 -146.42 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 MG A 392 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 96.8 REMARK 620 3 ASP A 245 OD2 110.4 115.2 REMARK 620 4 ASP A 287 OD2 139.5 93.3 100.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 391 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 81.9 REMARK 620 3 ASP A 255 OD1 104.9 91.5 REMARK 620 4 ASP A 255 OD2 166.2 95.4 61.5 REMARK 620 5 ASP A 257 OD1 87.1 166.4 83.7 93.5 REMARK 620 6 HOH A1001 O 98.4 95.4 156.4 95.3 94.0 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 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 392 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KBJ RELATED DB: PDB REMARK 900 ROOM TEMPERATURE X-RAY STRUCTURE OF APO-D-XYLOSE ISOMERASE REMARK 900 RELATED ID: 3KBM RELATED DB: PDB REMARK 900 ROOM TEMPERATURE X-RAY STRUCTURE OF D-XYLOSE ISOMERASE COMPLEXED REMARK 900 WITH 2CD(2+) CO-FACTORS AND D12-D-ALPHA-GLUCOSE IN THE CYCLIC FORM REMARK 900 RELATED ID: 3KBN RELATED DB: PDB REMARK 900 ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH REMARK 900 2NI(2+) CO-FACTORS AND D12-D-GLUCOSE IN THE LINEAR FORM REMARK 900 RELATED ID: 3KBS RELATED DB: PDB REMARK 900 ROOM TEMPERATURE X-RAY STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX REMARK 900 WITH 2CD(2+) CO-FACTORS REMARK 900 RELATED ID: 3KBV RELATED DB: PDB REMARK 900 ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH REMARK 900 2NI(2+) CO-FACTORS REMARK 900 RELATED ID: 3KCJ RELATED DB: PDB REMARK 900 ROOM TEMPERATURE NEUTRON STRUCTURE OF APO-D-XYLOSE ISOMERASE REMARK 900 (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBJ) REMARK 900 RELATED ID: 3KCL RELATED DB: PDB REMARK 900 ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX REMARK 900 WITH TWO CD2+ CATIONS AND D12-D-ALPHA-GLUCOSE IN THE RING FORM REMARK 900 (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBM) REMARK 900 RELATED ID: 3KCO RELATED DB: PDB REMARK 900 ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX REMARK 900 WITH TWO NI2+ CATIONS AND D12-D-GLUCOSE IN THE LINEAR FORM (REFINED REMARK 900 JOINTLY WITH X-RAY STRUCTURE 3KBN) DBREF 3KBW 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 391 1 HET MG A 392 1 HETNAM NI NICKEL (II) ION HETNAM MG MAGNESIUM ION FORMUL 2 NI NI 2+ FORMUL 3 MG MG 2+ FORMUL 4 HOH *312(H2 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 SER A 145 LYS A 149 5 5 HELIX 9 9 ASP A 150 GLY A 173 1 24 HELIX 10 10 THR A 195 GLU A 204 1 10 HELIX 11 11 ARG A 208 GLU A 210 5 3 HELIX 12 12 GLU A 217 MET A 223 1 7 HELIX 13 13 ASN A 227 ALA A 238 1 12 HELIX 14 14 ASP A 264 GLY A 279 1 16 HELIX 15 15 ASP A 295 ASP A 323 1 29 HELIX 16 16 ASP A 323 SER A 333 1 11 HELIX 17 17 ARG A 334 ALA A 339 1 6 HELIX 18 18 GLY A 346 ASP A 353 1 8 HELIX 19 19 ARG A 354 PHE A 357 5 4 HELIX 20 20 ASP A 361 ALA A 367 1 7 HELIX 21 21 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 ARG A 284 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 MG MG A 392 1555 1555 2.34 LINK OE2 GLU A 217 NI NI A 391 1555 1555 2.03 LINK OE1 GLU A 217 MG MG A 392 1555 1555 2.42 LINK NE2 HIS A 220 NI NI A 391 1555 1555 2.17 LINK OD2 ASP A 245 MG MG A 392 1555 1555 2.46 LINK OD1 ASP A 255 NI NI A 391 1555 1555 2.26 LINK OD2 ASP A 255 NI NI A 391 1555 1555 2.04 LINK OD1 ASP A 257 NI NI A 391 1555 1555 2.15 LINK OD2 ASP A 287 MG MG A 392 1555 1555 2.28 LINK NI NI A 391 O HOH A1001 1555 1555 2.03 CISPEP 1 GLU A 186 PRO A 187 0 13.61 SITE 1 AC1 5 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC1 5 HOH A1001 SITE 1 AC2 4 GLU A 181 GLU A 217 ASP A 245 ASP A 287 CRYST1 93.972 99.701 102.855 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 0.010641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010030 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009722 0.00000