HEADER ISOMERASE 02-MAY-06 2GVE TITLE TIME-OF-FLIGHT NEUTRON DIFFRACTION STRUCTURE OF D-XYLOSE ISOMERASE 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-BETA-ALPHA-BARRELS, TWO METAL BINDING SITES, PROTONATION KEYWDS 2 STATES OF RESIDUES, ISOMERASE EXPDTA NEUTRON DIFFRACTION AUTHOR A.K.KATZ,X.LI,H.L.CARRELL,B.L.HANSON,P.LANGAN,L.COATES, AUTHOR 2 B.P.SCHOENBORN,J.P.GLUSKER,G.J.BUNICK REVDAT 6 30-AUG-23 2GVE 1 REMARK SEQADV LINK REVDAT 5 18-OCT-17 2GVE 1 REMARK REVDAT 4 13-JUL-11 2GVE 1 VERSN REVDAT 3 24-FEB-09 2GVE 1 VERSN REVDAT 2 13-JUN-06 2GVE 1 JRNL REVDAT 1 16-MAY-06 2GVE 0 JRNL AUTH A.K.KATZ,X.LI,H.L.CARRELL,B.L.HANSON,P.LANGAN,L.COATES, JRNL AUTH 2 B.P.SCHOENBORN,J.P.GLUSKER,G.J.BUNICK JRNL TITL LOCATING ACTIVE-SITE HYDROGEN ATOMS IN D-XYLOSE ISOMERASE: JRNL TITL 2 TIME-OF-FLIGHT NEUTRON DIFFRACTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 8342 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16707576 JRNL DOI 10.1073/PNAS.0602598103 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.L.CARRELL,H.HOIER,J.P.GLUSKER REMARK 1 TITL MODES OF BINDING SUBSTRATES AND THEIR ANALOGS TO THE ENZYME REMARK 1 TITL 2 D-XYLOSE ISOMERASE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 50 113 1994 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15299449 REMARK 1 DOI 10.1107/S0907444993009345 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : 5%, RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.271 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1184 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 23312 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 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 : 2 REMARK 3 SOLVENT ATOMS : 512 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.032 REMARK 3 ANGLE DISTANCES (A) : 0.173 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.036 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.055 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.168 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GVE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037594. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 15-SEP-03 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 8.00 REMARK 230 NUMBER OF CRYSTALS USED : 2 REMARK 230 REMARK 230 NEUTRON SOURCE : NULL REMARK 230 BEAMLINE : NULL REMARK 230 WAVELENGTH OR RANGE (A) : 0.7-7.0 REMARK 230 MONOCHROMATOR : CHOPPER REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : AREA DETECTOR REMARK 230 DETECTOR MANUFACTURER : TIME-OF-FLIGHT MULTIWIRE HE3 REMARK 230 NEUTRON DETECTOR REMARK 230 INTENSITY-INTEGRATION SOFTWARE : D*TREK MODIFIED FOR NEUTRON TIME REMARK 230 -OF-FLIGHT LAUE REMARK 230 DATA SCALING SOFTWARE : D*TREK MODIFIED FOR NEUTRON TIME REMARK 230 -OF-FLIGHT LAUE REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 34394 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 230 RESOLUTION RANGE LOW (A) : 20.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 78.0 REMARK 230 DATA REDUNDANCY : NULL REMARK 230 R MERGE (I) : NULL REMARK 230 R SYM (I) : 0.18500 REMARK 230 FOR THE DATA SET : NULL 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) : 1.94 REMARK 230 COMPLETENESS FOR SHELL (%) : 39.0 REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : 0.26200 REMARK 230 FOR SHELL : NULL REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : SHELXL-97 REMARK 230 STARTING MODEL: 1XIB REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL,38%AMSO4,2MM MN2+ AND REMARK 280 2MM CO2+,XI @ 125MG/ML, PH 8.0, LIQUID DIFFUSION, TEMPERATURE REMARK 280 293K 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 46.94000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.84000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.45000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.94000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.84000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.45000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.94000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.84000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.45000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.94000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.84000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.45000 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 300 REMARK: HOMO-TETRAMER CONSISTING OF SUBUNITS RELATED BY REMARK 300 CRYSTALLOGRAPHIC 222 SYMMETRY 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 32780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45560 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 93.88000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 99.68000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 93.88000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 102.90000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 99.68000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 102.90000 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 A1094 LIES ON A SPECIAL POSITION. REMARK 375 O DOD A1279 LIES ON A SPECIAL POSITION. REMARK 375 O DOD A3335 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 OD2 ASP A 156 D2 DOD A 1250 1.33 REMARK 500 O LEU A 58 D1 DOD A 1204 1.34 REMARK 500 D1 DOD A 1220 O DOD A 1285 1.37 REMARK 500 O PRO A 60 HG SER A 63 1.38 REMARK 500 O PRO A 60 DG SER A 63 1.38 REMARK 500 OE2 GLU A 128 D2 DOD A 3038 1.40 REMARK 500 O ILE A 59 D1 DOD A 1133 1.41 REMARK 500 O DOD A 1163 D1 DOD A 1282 1.41 REMARK 500 O GLY A 62 D1 DOD A 3025 1.43 REMARK 500 OD1 ASP A 264 D2 DOD A 1058 1.43 REMARK 500 OD2 ASP A 110 D2 DOD A 1287 1.43 REMARK 500 D1 DOD A 1285 O DOD A 1341 1.44 REMARK 500 O PHE A 242 D2 DOD A 2010 1.44 REMARK 500 O DOD A 1223 D1 DOD A 1229 1.45 REMARK 500 OD2 ASP A 163 D1 DOD A 1228 1.48 REMARK 500 O TRP A 270 D1 DOD A 1114 1.49 REMARK 500 OD2 ASP A 264 D1 DOD A 1008 1.50 REMARK 500 D2 DOD A 1228 O DOD A 1271 1.50 REMARK 500 O DOD A 1059 D1 DOD A 1105 1.51 REMARK 500 D1 DOD A 1315 O DOD A 1316 1.51 REMARK 500 O GLY A 14 HG1 THR A 17 1.52 REMARK 500 O GLY A 14 DG1 THR A 17 1.52 REMARK 500 O DOD A 1091 D1 DOD A 1131 1.53 REMARK 500 O ILE A 252 D1 DOD A 1172 1.54 REMARK 500 D2 DOD A 1078 O DOD A 1088 1.54 REMARK 500 D1 DOD A 1076 O DOD A 1193 1.55 REMARK 500 OD2 ASP A 381 D2 DOD A 1127 1.55 REMARK 500 O DOD A 1009 D1 DOD A 1291 1.55 REMARK 500 O ARG A 157 D2 DOD A 1048 1.56 REMARK 500 O LEU A 34 D2 DOD A 1206 1.57 REMARK 500 O DOD A 1108 D1 DOD A 1206 1.57 REMARK 500 OE1 GLN A 249 D1 DOD A 1021 1.57 REMARK 500 OE2 GLU A 358 D1 DOD A 1360 1.58 REMARK 500 O DOD A 1348 D1 DOD A 3191 1.58 REMARK 500 D2 DOD A 1221 O DOD A 3309 1.60 REMARK 500 O PHE A 162 HH TYR A 212 1.60 REMARK 500 O PHE A 162 DH TYR A 212 1.60 REMARK 500 O PRO A 60 OG SER A 63 2.12 REMARK 500 O ASP A 273 OG SER A 277 2.17 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 OD2 ASP A 28 D2 DOD A 1208 3656 1.25 REMARK 500 OD2 ASP A 336 D1 DOD A 1032 7556 1.38 REMARK 500 O DOD A 1212 D1 DOD A 1323 2665 1.55 REMARK 500 D2 DOD A 1063 O DOD A 1092 4566 1.57 REMARK 500 O PRO A 25 D2 DOD A 1303 3656 1.59 REMARK 500 D2 DOD A 1041 O DOD A 1056 4566 1.59 REMARK 500 O PHE A 372 D2 DOD A 1071 3656 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 3 C GLN A 4 N 0.200 REMARK 500 GLU A 70 CB GLU A 70 CG 0.154 REMARK 500 GLU A 70 CD GLU A 70 OE1 0.112 REMARK 500 GLU A 70 CD GLU A 70 OE2 0.191 REMARK 500 GLU A 132 CD GLU A 132 OE1 0.108 REMARK 500 ARG A 340 CZ ARG A 340 NH2 0.078 REMARK 500 GLU A 359 CD GLU A 359 OE1 0.237 REMARK 500 GLU A 359 CD GLU A 359 OE2 0.121 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 GLU A 67 CG - CD - OE2 ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 68 CD - NE - CZ ANGL. DEV. = -11.5 DEGREES REMARK 500 ARG A 68 NH1 - CZ - NH2 ANGL. DEV. = -12.4 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -9.6 DEGREES REMARK 500 ARG A 76 NH1 - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 113 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 157 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 188 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 205 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR A 212 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 259 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 266 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 284 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 284 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 292 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 316 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 316 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 331 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 340 CD - NE - CZ ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 354 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 354 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 368 NE - CZ - NH2 ANGL. DEV. = -5.6 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 THR A 17 -80.22 -66.64 REMARK 500 PHE A 94 -30.91 -135.62 REMARK 500 GLU A 186 124.93 77.79 REMARK 500 ASN A 215 76.68 -117.47 REMARK 500 ASN A 247 -165.93 -179.07 REMARK 500 LYS A 253 -169.42 170.81 REMARK 500 PRO A 341 151.68 -49.90 REMARK 500 PHE A 357 -67.84 -150.68 REMARK 500 ALA A 386 71.41 -116.19 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 41 0.15 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 CO A 391 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 93.7 REMARK 620 3 ASP A 245 OD2 96.8 116.7 REMARK 620 4 ASP A 287 OD2 161.5 91.5 96.6 REMARK 620 5 DOD A1116 O 72.5 114.5 128.2 89.2 REMARK 620 6 DOD A1218 O 102.1 163.0 67.9 71.5 65.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 390 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 ASP A 255 OD2 151.4 REMARK 620 3 ASP A 257 OD1 91.5 101.6 REMARK 620 4 DOD A1018 O 97.7 106.5 94.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 391 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XIB RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF XYLOSE ISOMERASE USED FOR STARTING NEUTRON REMARK 900 REFINEMENT REMARK 900 RELATED ID: 2GLK RELATED DB: PDB REMARK 900 0.94 ANGSTROM X-RAY STRUCTURE OF XYLOSE ISOMERASE AT 100K REMARK 900 RELATED ID: 2GUB RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF METAL FREE XYLOSE ISOMERASE DBREF 2GVE A 2 388 UNP P24300 XYLA_STRRU 1 387 SEQADV 2GVE MET A 1 UNP P24300 INITIATING METHIONINE 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 CO A 390 1 HET CO A 391 1 HETNAM CO COBALT (II) ION FORMUL 2 CO 2(CO 2+) FORMUL 4 DOD *512(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 ASP A 336 ARG A 340 5 5 HELIX 17 17 GLY A 346 ASP A 352 1 7 HELIX 18 18 ASP A 353 PHE A 357 5 5 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 MET A 88 THR A 90 1 N ALA A 89 O THR A 133 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 CO CO A 391 1555 1555 2.00 LINK OE2 GLU A 217 CO CO A 390 1555 1555 2.09 LINK OE1 GLU A 217 CO CO A 391 1555 1555 1.99 LINK OD2 ASP A 245 CO CO A 391 1555 1555 2.48 LINK OD2 ASP A 255 CO CO A 390 1555 1555 1.94 LINK OD1 ASP A 257 CO CO A 390 1555 1555 2.20 LINK OD2 ASP A 287 CO CO A 391 1555 1555 2.05 LINK CO CO A 390 O DOD A1018 1555 1555 1.97 LINK CO CO A 391 O DOD A1116 1555 1555 2.47 LINK CO CO A 391 O DOD A1218 1555 1555 2.22 CISPEP 1 GLU A 186 PRO A 187 0 2.70 SITE 1 AC1 5 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC1 5 DOD A1018 SITE 1 AC2 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AC2 6 DOD A1116 DOD A1218 CRYST1 93.880 99.680 102.900 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 0.010652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010032 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009718 0.00000