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 6 30-AUG-23 2GLK 1 REMARK SEQADV LINK 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,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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 506 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 95.0 REMARK 620 3 ASP A 245 OD2 91.4 112.4 REMARK 620 4 ASP A 287 OD2 160.8 89.7 103.9 REMARK 620 5 GOL A 601 O2 86.6 161.5 86.0 83.2 REMARK 620 6 HOH A1121 O 81.6 90.3 156.8 79.8 71.6 REMARK 620 N 1 2 3 4 5 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 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 77.7 REMARK 620 3 ASP A 255 OD2 164.9 99.5 REMARK 620 4 ASP A 255 OD1 121.7 123.6 47.8 REMARK 620 5 ASP A 255 OD1 106.4 101.5 59.4 26.3 REMARK 620 6 ASP A 257 OD1 90.5 168.1 92.2 63.4 82.3 REMARK 620 7 HOH A1316 O 95.7 98.6 99.4 126.9 152.8 81.8 REMARK 620 N 1 2 3 4 5 6 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 OE2AGLU A 181 MN MN A 506 1555 1555 2.07 LINK OE2 GLU A 217 MN MN A 505 1555 1555 2.05 LINK OE1 GLU A 217 MN MN A 506 1555 1555 2.21 LINK NE2 HIS A 220 MN MN A 505 1555 1555 2.76 LINK OD2 ASP A 245 MN MN A 506 1555 1555 2.32 LINK OD2BASP A 255 MN MN A 505 1555 1555 2.03 LINK OD1AASP A 255 MN MN A 505 1555 1555 2.48 LINK OD1BASP A 255 MN MN A 505 1555 1555 2.31 LINK OD1AASP A 257 MN MN A 505 1555 1555 2.20 LINK OD2 ASP A 287 MN MN A 506 1555 1555 2.18 LINK MN MN A 505 O HOH A1316 1555 1555 2.21 LINK MN MN A 506 O2 GOL A 601 1555 1555 2.39 LINK MN MN A 506 O HOH A1121 1555 1555 2.44 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