HEADER ISOMERASE 21-OCT-09 3KCO TITLE ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX TITLE 2 WITH TWO NI2+ CATIONS AND D12-D-GLUCOSE IN THE LINEAR FORM (REFINED TITLE 3 JOINTLY WITH X-RAY STRUCTURE 3KBN) 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, DEUTERATED GLUCOSE, CARBOHYDRATE METABOLISM, METAL- KEYWDS 2 BINDING, PENTOSE SHUNT, XYLOSE METABOLISM, ISOMERASE EXPDTA NEUTRON DIFFRACTION; X-RAY DIFFRACTION AUTHOR A.Y.KOVALEVSKY,P.LANGAN REVDAT 9 03-APR-24 3KCO 1 REMARK REVDAT 8 21-FEB-24 3KCO 1 HETSYN REVDAT 7 29-JUL-20 3KCO 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 SITE REVDAT 6 20-JUN-18 3KCO 1 REMARK REVDAT 5 25-APR-18 3KCO 1 REMARK REVDAT 4 27-JUL-11 3KCO 1 REMARK REVDAT REVDAT 3 13-JUL-11 3KCO 1 VERSN REVDAT 2 23-MAR-11 3KCO 1 JRNL REVDAT 1 16-JUN-10 3KCO 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NCNS 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 NEUTRON DATA. 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)) : 3.000 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 : 27031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.273 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1388 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL 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 : 15 REMARK 3 SOLVENT ATOMS : 309 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.011 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 OTHER REFINEMENT REMARKS: NULL REMARK 3 X-RAY DATA. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 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 : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3281 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL 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 : 15 REMARK 3 SOLVENT ATOMS : 309 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KCO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 : D*TREK MODIFIED FOR NEUTRON REMARK 200 DATA SCALING SOFTWARE : LAUENORM MODIFIED FOR NEUTRON REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NCNS REMARK 200 STARTING MODEL: 3CWH REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 10-OCT-08 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 7.70 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : PCS REMARK 230 WAVELENGTH OR RANGE (A) : 0.7-6.5 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : AREA DETECTOR REMARK 230 DETECTOR MANUFACTURER : TIME-OF-FLIGHT MULTIWIRE HE3 REMARK 230 INTENSITY-INTEGRATION SOFTWARE : D*TREK MODIFIED FOR NEUTRON REMARK 230 DATA SCALING SOFTWARE : LAUENORM MODIFIED FOR NEUTRON REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 27031 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 230 RESOLUTION RANGE LOW (A) : 20.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 72.0 REMARK 230 DATA REDUNDANCY : 3.200 REMARK 230 R MERGE (I) : NULL REMARK 230 R SYM (I) : 0.23600 REMARK 230 FOR THE DATA SET : 4.0000 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 (%) : 72.5 REMARK 230 DATA REDUNDANCY IN SHELL : 1.90 REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : 0.35900 REMARK 230 FOR SHELL : 1.500 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : NCNS REMARK 230 STARTING MODEL: 3CWH REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES, 40% V/V (NH4)2SO4 (SAT.), REMARK 280 PROTEIN 40 MG/ML, PH=7.7, BATCH METHOD, APO-XI CRYSTALS WERE REMARK 280 SOAKED WITH 5MM NICL2 SALT, 0.5M PER-DEUTERATED D-GLUCOSE IN D2O, REMARK 280 TEMPERATURE 293K, PH 7.7 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 47.00350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.83450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.43100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.00350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.83450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.43100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.00350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.83450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.43100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.00350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.83450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.43100 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: 35010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -347.0 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 -102.86200 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 -102.86200 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 A1192 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: 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 D2 DOD A 1185 O DOD A 1225 1.37 REMARK 500 O DOD A 1105 D2 DOD A 1154 1.53 REMARK 500 O DOD A 1185 D1 DOD A 1273 1.54 REMARK 500 D1 DOD A 1216 O DOD A 1251 1.59 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 -73.84 -81.88 REMARK 500 ASP A 175 67.33 -109.29 REMARK 500 GLU A 186 99.80 74.58 REMARK 500 LEU A 193 61.35 61.37 REMARK 500 ASN A 247 -164.93 -168.87 REMARK 500 LYS A 253 -166.36 -174.65 REMARK 500 PHE A 357 -72.81 -165.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 331 0.07 SIDE CHAIN 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 393 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 95.9 REMARK 620 3 ASP A 245 OD2 97.0 101.3 REMARK 620 4 ASP A 287 OD2 160.5 97.1 94.5 REMARK 620 5 GLO A 401 O4 81.1 167.2 91.5 83.0 REMARK 620 6 GLO A 401 O2 81.7 81.4 177.1 86.0 85.8 REMARK 620 N 1 2 3 4 5 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 83.4 REMARK 620 3 GLO A 401 O1 169.6 90.6 REMARK 620 4 GLO A 401 O2 111.7 107.4 78.1 REMARK 620 5 DOD A1001 O 102.6 170.6 82.3 77.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 392 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 73.1 REMARK 620 3 ASP A 255 OD1 122.9 101.3 REMARK 620 4 ASP A 255 OD2 175.1 106.1 61.9 REMARK 620 5 ASP A 257 OD1 94.0 166.1 81.0 87.2 REMARK 620 6 DOD A1001 O 82.6 93.5 153.3 92.7 90.0 REMARK 620 N 1 2 3 4 5 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: 3KBW RELATED DB: PDB REMARK 900 ROOM TEMPERATURE X-RAY MIXED-METAL STRUCTURE OF D-XYLOSE ISOMERASE REMARK 900 IN COMPLEX WITH NI(2+) AND MG(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) DBREF 3KCO 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 NI A 392 1 HET NI A 393 1 HET GLO A 401 23 HETNAM NI NICKEL (II) ION HETNAM GLO D-GLUCOSE HETSYN GLO D-GLUCOSE IN LINEAR FORM FORMUL 2 NI 3(NI 2+) FORMUL 5 GLO C6 H12 O6 FORMUL 6 DOD *309(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 LEU A 46 1 12 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 ALA A 278 1 15 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 LEU A 384 1 14 SHEET 1 A 8 TYR A 212 VAL A 214 0 SHEET 2 A 8 ARG A 177 ILE A 180 1 N PHE A 178 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 LYS A 85 THR A 90 1 N ALA A 89 O VAL A 135 SHEET 5 A 8 GLY A 50 HIS A 54 1 N VAL A 51 O LYS A 85 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 393 1555 1555 2.05 LINK OE2 GLU A 217 NI NI A 391 1555 1555 2.28 LINK OE2 GLU A 217 NI NI A 392 1555 1555 2.17 LINK OE1 GLU A 217 NI NI A 393 1555 1555 2.02 LINK NE2 HIS A 220 NI NI A 391 1555 1555 2.02 LINK NE2 HIS A 220 NI NI A 392 1555 1555 2.61 LINK OD2 ASP A 245 NI NI A 393 1555 1555 2.22 LINK OD1 ASP A 255 NI NI A 392 1555 1555 2.18 LINK OD2 ASP A 255 NI NI A 392 1555 1555 2.08 LINK OD1 ASP A 257 NI NI A 392 1555 1555 2.23 LINK OD2 ASP A 287 NI NI A 393 1555 1555 2.11 LINK NI NI A 391 O1 GLO A 401 1555 1555 2.29 LINK NI NI A 391 O2 GLO A 401 1555 1555 2.04 LINK NI NI A 391 O DOD A1001 1555 1555 1.88 LINK NI NI A 392 O DOD A1001 1555 1555 2.72 LINK NI NI A 393 O4 GLO A 401 1555 1555 2.38 LINK NI NI A 393 O2 GLO A 401 1555 1555 2.16 CISPEP 1 GLU A 186 PRO A 187 0 28.64 CRYST1 94.007 99.669 102.862 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 0.010638 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009722 0.00000