HEADER ISOMERASE 05-APR-06 2GLK TITLE HIGH-RESOLUTION STUDY OF D-XYLOSE ISOMERASE, 0.94A RESOLUTION. 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, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.KATZ,H.L.CARRELL,B.L.HANSON,J.M.HARP,J.P.GLUSKER,G.J.BUNICK REVDAT 5 18-OCT-17 2GLK 1 REMARK REVDAT 4 13-JUL-11 2GLK 1 VERSN REVDAT 3 24-FEB-09 2GLK 1 VERSN REVDAT 2 13-JUN-06 2GLK 1 JRNL REVDAT 1 16-MAY-06 2GLK 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 2 REMARK 2 RESOLUTION. 0.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 231037 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.116 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.128 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 21042 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2829 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 14.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.4100 REMARK 3 BIN FREE R VALUE SET COUNT : 252 REMARK 3 BIN FREE R VALUE : 0.4220 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 : 26 REMARK 3 SOLVENT ATOMS : 426 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.016 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.016 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.008 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.304 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3263 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2939 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4406 ; 1.917 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6801 ; 1.869 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ; 5.472 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;32.824 ;22.903 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 534 ;12.414 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;13.787 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3717 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 746 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 722 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2970 ; 0.205 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1627 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1679 ; 0.095 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 275 ; 0.176 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 21 ; 0.300 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 198 ; 0.340 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.207 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2506 ; 2.118 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 806 ; 1.316 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3112 ; 2.560 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1520 ; 3.436 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1294 ; 4.695 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3805 ; 1.842 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 429 ;11.867 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3031 ; 5.914 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2GLK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 252079 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.940 REMARK 200 RESOLUTION RANGE LOW (A) : 35.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.6 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) : 0.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 12.0 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1XIB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL,25%AMSO4,2MM MN2+ AND REMARK 280 2MM CO2+ , XI @ 25MG/ML., PH 8, VAPOR DIFFUSION, TEMPERATURE 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 46.35600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.96750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 50.93350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.35600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.96750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.93350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.35600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.96750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.93350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.35600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.96750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.93350 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: 36600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -180.0 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 92.71200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 97.93500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 92.71200 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 101.86700 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 97.93500 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 101.86700 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 A1147 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 HOH A 1489 O HOH A 1490 1.74 REMARK 500 O HOH A 1093 O HOH A 1164 1.75 REMARK 500 O HOH A 1270 O HOH A 1388 2.02 REMARK 500 O HOH A 1197 O HOH A 1421 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 O HOH A 1333 O HOH A 1449 2665 2.10 REMARK 500 O HOH A 1282 O HOH A 1459 3656 2.19 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 ASP A 56 CB ASP A 56 CG 0.201 REMARK 500 GLU A 181 CB GLU A 181 CG -0.120 REMARK 500 GLU A 181 CD GLU A 181 OE1 0.139 REMARK 500 GLU A 186 CD GLU A 186 OE2 0.088 REMARK 500 ASP A 255 CB ASP A 255 CG -0.208 REMARK 500 ASP A 257 CB ASP A 257 CG 0.288 REMARK 500 ASP A 257 CB ASP A 257 CG -0.254 REMARK 500 GLU A 337 CB GLU A 337 CG -0.155 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 ASP A 24 CB - CA - C ANGL. DEV. = 14.9 DEGREES REMARK 500 PHE A 26 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 PHE A 26 N - CA - CB ANGL. DEV. = 13.1 DEGREES REMARK 500 PHE A 26 CB - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 PHE A 26 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 56 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 76 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 GLU A 186 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 TYR A 212 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 TYR A 212 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 255 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 ASP A 255 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ASP A 257 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 257 CB - CG - OD1 ANGL. DEV. = -8.1 DEGREES REMARK 500 ASP A 257 CB - CG - OD2 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 266 CD - NE - CZ ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 374 NE - CZ - NH1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 374 NE - CZ - NH2 ANGL. DEV. = 3.9 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 ASN A 2 43.69 -144.54 REMARK 500 THR A 17 -76.68 -84.09 REMARK 500 PHE A 94 -27.00 -140.26 REMARK 500 GLU A 186 101.89 82.81 REMARK 500 ASN A 247 -169.56 -168.16 REMARK 500 TYR A 254 158.23 -48.42 REMARK 500 ALA A 343 61.69 -151.15 REMARK 500 PHE A 357 -78.51 -153.53 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 MN A 505 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 255 OD2 REMARK 620 2 GLU A 217 OE2 164.9 REMARK 620 3 ASP A 257 OD1 92.2 90.5 REMARK 620 4 HIS A 220 NE2 99.5 77.7 168.1 REMARK 620 5 HOH A1316 O 99.4 95.7 81.8 98.6 REMARK 620 6 ASP A 255 OD1 47.8 121.7 63.4 123.6 126.9 REMARK 620 7 ASP A 255 OD1 59.4 106.4 82.3 101.5 152.8 26.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 506 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 287 OD2 REMARK 620 2 GLU A 181 OE2 160.8 REMARK 620 3 GLU A 217 OE1 89.7 95.0 REMARK 620 4 ASP A 245 OD2 103.9 91.4 112.4 REMARK 620 5 HOH A1121 O 79.8 81.6 90.3 156.8 REMARK 620 6 GOL A 601 O2 83.2 86.6 161.5 86.0 71.6 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 MN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XIB RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE AT 1.6 A RESOLUTION AT 4 C. USED AS STARTING REMARK 900 MODEL FOR THIS STUDY DBREF 2GLK A 2 388 UNP P24300 XYLA_STRRU 1 387 SEQADV 2GLK 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 MN A 505 1 HET MN A 506 1 HET GOL A 601 6 HET GOL A 602 6 HET GOL A 603 6 HET GOL A 604 6 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN 2(MN 2+) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 HOH *426(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 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 LEU A 129 1 22 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 ARG A 368 1 8 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 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 MN MN A 505 OD2BASP A 255 1555 1555 2.03 LINK MN MN A 505 OE2 GLU A 217 1555 1555 2.05 LINK MN MN A 506 OD2 ASP A 287 1555 1555 2.18 LINK MN MN A 506 OE2AGLU A 181 1555 1555 2.07 LINK MN MN A 505 OD1AASP A 257 1555 1555 2.20 LINK MN MN A 506 OE1 GLU A 217 1555 1555 2.21 LINK MN MN A 506 OD2 ASP A 245 1555 1555 2.32 LINK MN MN A 505 NE2 HIS A 220 1555 1555 2.76 LINK MN MN A 505 O HOH A1316 1555 1555 2.21 LINK MN MN A 506 O HOH A1121 1555 1555 2.44 LINK MN MN A 506 O2 GOL A 601 1555 1555 2.39 LINK OD1AASP A 255 MN MN A 505 1555 1555 2.48 LINK OD1BASP A 255 MN MN A 505 1555 1555 2.31 CISPEP 1 MET A 1 ASN A 2 0 8.23 CISPEP 2 MET A 1 ASN A 2 0 -1.88 CISPEP 3 GLU A 186 PRO A 187 0 21.47 SITE 1 AC1 5 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC1 5 HOH A1316 SITE 1 AC2 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AC2 6 GOL A 601 HOH A1121 SITE 1 AC3 11 TRP A 16 HIS A 54 TRP A 137 GLU A 181 SITE 2 AC3 11 ASP A 245 ASP A 287 MN A 506 HOH A1028 SITE 3 AC3 11 HOH A1048 HOH A1121 HOH A1387 SITE 1 AC4 5 ASP A 9 GLU A 276 ARG A 284 LYS A 314 SITE 2 AC4 5 HOH A1325 SITE 1 AC5 8 ASP A 24 PRO A 25 TYR A 254 GLN A 256 SITE 2 AC5 8 HOH A1061 HOH A1086 HOH A1131 HOH A1422 SITE 1 AC6 9 GLY A 146 LYS A 149 VAL A 151 HIS A 230 SITE 2 AC6 9 HOH A1015 HOH A1031 HOH A1469 HOH A1474 SITE 3 AC6 9 HOH A1481 CRYST1 92.712 97.935 101.867 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 0.010786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009817 0.00000 MASTER 455 0 6 21 10 0 14 6 0 0 0 30 END