HEADER ISOMERASE 26-NOV-02 1O8B TITLE STRUCTURE OF ESCHERICHIA COLI RIBOSE-5-PHOSPHATE ISOMERASE, RPIA, TITLE 2 COMPLEXED WITH ARABINOSE-5-PHOSPHATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSE 5-PHOSPHATE ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHORIBOISOMERASE A, RPIA; COMPND 5 EC: 5.3.1.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ISOMERASE, RIBOSE PHOSPHATE ISOMERASE, RPIA, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, MCSG, MIDWEST CENTER FOR STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR R.-G.ZHANG,C.E.ANDERSSON,A.SAVCHENKO,T.SKARINA,E.EVDOKIMOVA, AUTHOR 2 S.BEASLEY,C.H.ARROWSMITH,A.M.EDWARDS,A.JOACHIMIAK,S.L.MOWBRAY, AUTHOR 3 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 10 23-OCT-24 1O8B 1 REMARK REVDAT 9 13-DEC-23 1O8B 1 HETSYN REVDAT 8 29-JUL-20 1O8B 1 COMPND REMARK HETNAM SITE REVDAT 8 2 1 ATOM REVDAT 7 21-AUG-19 1O8B 1 REMARK LINK REVDAT 6 13-JUL-11 1O8B 1 VERSN REVDAT 5 01-SEP-09 1O8B 1 VERSN REVDAT 4 24-FEB-09 1O8B 1 VERSN REVDAT 3 31-JAN-05 1O8B 1 KEYWDS REVDAT 2 19-JAN-05 1O8B 1 KEYWDS AUTHOR REMARK REVDAT 1 24-JAN-03 1O8B 0 JRNL AUTH R.-G.ZHANG,C.E.ANDERSSON,A.SAVCHENKO,T.SKARINA,E.EVDOKIMOVA, JRNL AUTH 2 S.BEASLEY,C.H.ARROWSMITH,A.M.EDWARDS,A.JOACHIMIAK, JRNL AUTH 3 S.L.MOWBRAY JRNL TITL STRUCTURE OF ESCHERICHIA COLI RIBOSE-5-PHOSPHATE ISOMERASE: JRNL TITL 2 A UBIQUITOUS ENZYME OF THE PENTOSE PHOSPHATE PATHWAY AND THE JRNL TITL 3 CALVIN CYCLE JRNL REF STRUCTURE V. 11 31 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12517338 JRNL DOI 10.1016/S0969-2126(02)00933-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.HOVE-JENSEN,M.MAIGAARD REMARK 1 TITL ESCHERICHIA COLI RPIA GENE ENCODING RIBOSE PHOSPHATE REMARK 1 TITL 2 ISOMERASE A REMARK 1 REF J.BACTERIOL. V. 175 5628 1993 REMARK 1 REFN ISSN 0021-9193 REMARK 1 PMID 8366047 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 3 NUMBER OF REFLECTIONS : 86708 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4498 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2767 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 136 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2771 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.54000 REMARK 3 B22 (A**2) : -0.48000 REMARK 3 B33 (A**2) : 0.89000 REMARK 3 B12 (A**2) : -0.68000 REMARK 3 B13 (A**2) : 0.25000 REMARK 3 B23 (A**2) : -0.30000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.076 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2828 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 3829 ; 1.863 ; 1.981 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 460 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2041 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1223 ; 0.220 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 260 ; 0.116 ; 0.500 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): 22 ; 0.161 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.507 ; 0.500 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): 1861 ; 0.775 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2982 ; 1.147 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 967 ; 2.236 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 847 ; 3.122 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 23 A 31 REMARK 3 ORIGIN FOR THE GROUP (A): 3.2535 -4.3999 -7.1036 REMARK 3 T TENSOR REMARK 3 T11: 0.1241 T22: 0.1251 REMARK 3 T33: 0.1088 T12: -0.0229 REMARK 3 T13: 0.0754 T23: -0.0766 REMARK 3 L TENSOR REMARK 3 L11: 13.6612 L22: 14.4295 REMARK 3 L33: 6.6576 L12: 12.8122 REMARK 3 L13: -3.3693 L23: -8.0774 REMARK 3 S TENSOR REMARK 3 S11: -0.8782 S12: 0.7406 S13: -0.7833 REMARK 3 S21: -0.7150 S22: 0.4396 S23: -0.8107 REMARK 3 S31: 0.6265 S32: -0.0782 S33: 0.4386 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 47 A 55 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1763 -3.2891 -7.8715 REMARK 3 T TENSOR REMARK 3 T11: 0.1102 T22: 0.1260 REMARK 3 T33: 0.2292 T12: -0.0465 REMARK 3 T13: 0.0942 T23: -0.1247 REMARK 3 L TENSOR REMARK 3 L11: 31.6244 L22: 3.7495 REMARK 3 L33: 4.3765 L12: -0.3751 REMARK 3 L13: -8.3084 L23: -0.0229 REMARK 3 S TENSOR REMARK 3 S11: -1.1248 S12: 1.0320 S13: -2.1034 REMARK 3 S21: -0.0455 S22: 0.4302 S23: -0.1840 REMARK 3 S31: 0.4329 S32: -0.2102 S33: 0.6946 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 68 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8573 2.6860 -2.9094 REMARK 3 T TENSOR REMARK 3 T11: 0.0477 T22: 0.0697 REMARK 3 T33: 0.0320 T12: -0.0225 REMARK 3 T13: -0.0353 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 3.4411 L22: 1.4398 REMARK 3 L33: 2.7794 L12: 1.0103 REMARK 3 L13: -1.9015 L23: -0.3453 REMARK 3 S TENSOR REMARK 3 S11: -0.1475 S12: 0.3077 S13: 0.0789 REMARK 3 S21: -0.2411 S22: 0.1463 S23: 0.1025 REMARK 3 S31: 0.0460 S32: -0.0314 S33: 0.0012 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 99 A 218 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6343 1.9889 8.1974 REMARK 3 T TENSOR REMARK 3 T11: 0.0181 T22: 0.0129 REMARK 3 T33: 0.0540 T12: 0.0015 REMARK 3 T13: -0.0063 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 1.3097 L22: 0.9522 REMARK 3 L33: 1.0099 L12: 0.1935 REMARK 3 L13: -0.1386 L23: -0.2435 REMARK 3 S TENSOR REMARK 3 S11: -0.0261 S12: 0.0896 S13: -0.0615 REMARK 3 S21: -0.0258 S22: 0.0546 S23: 0.1684 REMARK 3 S31: 0.0769 S32: -0.0883 S33: -0.0285 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 17 REMARK 3 ORIGIN FOR THE GROUP (A): 25.8456 28.3513 31.5816 REMARK 3 T TENSOR REMARK 3 T11: 0.1067 T22: 0.0489 REMARK 3 T33: 0.0121 T12: -0.0292 REMARK 3 T13: -0.0156 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 5.6936 L22: 5.8930 REMARK 3 L33: 6.0227 L12: 3.8307 REMARK 3 L13: -2.7468 L23: -2.9626 REMARK 3 S TENSOR REMARK 3 S11: 0.1810 S12: -0.2243 S13: 0.0527 REMARK 3 S21: 0.3466 S22: -0.2783 S23: -0.2056 REMARK 3 S31: 0.0252 S32: 0.1664 S33: 0.0973 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 22 B 97 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5236 15.8776 29.3018 REMARK 3 T TENSOR REMARK 3 T11: 0.1257 T22: 0.0618 REMARK 3 T33: 0.0482 T12: -0.0094 REMARK 3 T13: -0.0173 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 1.4978 L22: 2.3325 REMARK 3 L33: 1.9561 L12: 0.2604 REMARK 3 L13: 0.5624 L23: -0.5224 REMARK 3 S TENSOR REMARK 3 S11: 0.1062 S12: -0.2402 S13: -0.1376 REMARK 3 S21: 0.4160 S22: -0.0848 S23: -0.1350 REMARK 3 S31: 0.1433 S32: 0.0463 S33: -0.0214 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 99 B 218 REMARK 3 ORIGIN FOR THE GROUP (A): 14.5400 21.0438 13.0985 REMARK 3 T TENSOR REMARK 3 T11: 0.0093 T22: 0.0168 REMARK 3 T33: 0.0378 T12: 0.0065 REMARK 3 T13: 0.0101 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.6919 L22: 1.0107 REMARK 3 L33: 0.9583 L12: 0.2348 REMARK 3 L13: 0.1302 L23: 0.2390 REMARK 3 S TENSOR REMARK 3 S11: 0.0280 S12: 0.0192 S13: 0.1074 REMARK 3 S21: 0.0115 S22: -0.0091 S23: 0.0084 REMARK 3 S31: -0.0617 S32: 0.0437 S33: -0.0189 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ELECTRON DENSITY COULD NOT BE OBSERVED REMARK 3 FOR RESIDUES 1-22, 32-46, 56-67, 98 AND 219 IN MOLECULE A AND REMARK 3 RESIDUES 1,18-21, 98 AND 219 IN MOLECULE B. THESE RESIDUES WERE REMARK 3 OMITTED AND ARE NOT PRESENT IN THE MODEL. REMARK 4 REMARK 4 1O8B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1290011707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : GE(220),HORIZONTAL FOCUSING REMARK 200 MULTILAYER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90067 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.76000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1KS2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN FROM A SOLUTION REMARK 280 CONTAINING 3.5 MG/ML PROTEIN, 30-35 % PEG 4000 10 MM ARABINOSE-5- REMARK 280 PHOSPHATE, 0.05M TRIS-HCL PH 8.4, 0.1 M MGCL2, PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A 1 REMARK 465 THR A 2 REMARK 465 GLN A 3 REMARK 465 ASP A 4 REMARK 465 GLU A 5 REMARK 465 LEU A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 ALA A 9 REMARK 465 VAL A 10 REMARK 465 GLY A 11 REMARK 465 TRP A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 GLN A 16 REMARK 465 TYR A 17 REMARK 465 VAL A 18 REMARK 465 GLN A 19 REMARK 465 PRO A 20 REMARK 465 GLY A 21 REMARK 465 THR A 22 REMARK 465 ALA A 32 REMARK 465 ALA A 33 REMARK 465 HIS A 34 REMARK 465 PHE A 35 REMARK 465 ILE A 36 REMARK 465 ASP A 37 REMARK 465 ALA A 38 REMARK 465 LEU A 39 REMARK 465 GLY A 40 REMARK 465 THR A 41 REMARK 465 MSE A 42 REMARK 465 LYS A 43 REMARK 465 GLY A 44 REMARK 465 GLN A 45 REMARK 465 ILE A 46 REMARK 465 SER A 56 REMARK 465 THR A 57 REMARK 465 GLU A 58 REMARK 465 LYS A 59 REMARK 465 LEU A 60 REMARK 465 LYS A 61 REMARK 465 SER A 62 REMARK 465 LEU A 63 REMARK 465 GLY A 64 REMARK 465 ILE A 65 REMARK 465 HIS A 66 REMARK 465 VAL A 67 REMARK 465 ALA A 98 REMARK 465 LYS A 219 REMARK 465 MSE B 1 REMARK 465 VAL B 18 REMARK 465 GLN B 19 REMARK 465 PRO B 20 REMARK 465 GLY B 21 REMARK 465 ALA B 98 REMARK 465 LYS B 219 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 ASN B 164 O HOH B 2064 2.18 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 B 204 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2008 DISTANCE = 6.75 ANGSTROMS REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LKZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D-RIBOSE-5-PHOSPHATE ISOMERASE (RPIA)FROM REMARK 900 ESCHERICHIA COLI. REMARK 900 RELATED ID: APC065 RELATED DB: TARGETDB DBREF 1O8B A 1 219 UNP P0A7Z0 RPIA_ECOLI 1 219 DBREF 1O8B B 1 219 UNP P0A7Z0 RPIA_ECOLI 1 219 SEQRES 1 A 219 MSE THR GLN ASP GLU LEU LYS LYS ALA VAL GLY TRP ALA SEQRES 2 A 219 ALA LEU GLN TYR VAL GLN PRO GLY THR ILE VAL GLY VAL SEQRES 3 A 219 GLY THR GLY SER THR ALA ALA HIS PHE ILE ASP ALA LEU SEQRES 4 A 219 GLY THR MSE LYS GLY GLN ILE GLU GLY ALA VAL SER SER SEQRES 5 A 219 SER ASP ALA SER THR GLU LYS LEU LYS SER LEU GLY ILE SEQRES 6 A 219 HIS VAL PHE ASP LEU ASN GLU VAL ASP SER LEU GLY ILE SEQRES 7 A 219 TYR VAL ASP GLY ALA ASP GLU ILE ASN GLY HIS MSE GLN SEQRES 8 A 219 MSE ILE LYS GLY GLY GLY ALA ALA LEU THR ARG GLU LYS SEQRES 9 A 219 ILE ILE ALA SER VAL ALA GLU LYS PHE ILE CYS ILE ALA SEQRES 10 A 219 ASP ALA SER LYS GLN VAL ASP ILE LEU GLY LYS PHE PRO SEQRES 11 A 219 LEU PRO VAL GLU VAL ILE PRO MSE ALA ARG SER ALA VAL SEQRES 12 A 219 ALA ARG GLN LEU VAL LYS LEU GLY GLY ARG PRO GLU TYR SEQRES 13 A 219 ARG GLN GLY VAL VAL THR ASP ASN GLY ASN VAL ILE LEU SEQRES 14 A 219 ASP VAL HIS GLY MSE GLU ILE LEU ASP PRO ILE ALA MSE SEQRES 15 A 219 GLU ASN ALA ILE ASN ALA ILE PRO GLY VAL VAL THR VAL SEQRES 16 A 219 GLY LEU PHE ALA ASN ARG GLY ALA ASP VAL ALA LEU ILE SEQRES 17 A 219 GLY THR PRO ASP GLY VAL LYS THR ILE VAL LYS SEQRES 1 B 219 MSE THR GLN ASP GLU LEU LYS LYS ALA VAL GLY TRP ALA SEQRES 2 B 219 ALA LEU GLN TYR VAL GLN PRO GLY THR ILE VAL GLY VAL SEQRES 3 B 219 GLY THR GLY SER THR ALA ALA HIS PHE ILE ASP ALA LEU SEQRES 4 B 219 GLY THR MSE LYS GLY GLN ILE GLU GLY ALA VAL SER SER SEQRES 5 B 219 SER ASP ALA SER THR GLU LYS LEU LYS SER LEU GLY ILE SEQRES 6 B 219 HIS VAL PHE ASP LEU ASN GLU VAL ASP SER LEU GLY ILE SEQRES 7 B 219 TYR VAL ASP GLY ALA ASP GLU ILE ASN GLY HIS MSE GLN SEQRES 8 B 219 MSE ILE LYS GLY GLY GLY ALA ALA LEU THR ARG GLU LYS SEQRES 9 B 219 ILE ILE ALA SER VAL ALA GLU LYS PHE ILE CYS ILE ALA SEQRES 10 B 219 ASP ALA SER LYS GLN VAL ASP ILE LEU GLY LYS PHE PRO SEQRES 11 B 219 LEU PRO VAL GLU VAL ILE PRO MSE ALA ARG SER ALA VAL SEQRES 12 B 219 ALA ARG GLN LEU VAL LYS LEU GLY GLY ARG PRO GLU TYR SEQRES 13 B 219 ARG GLN GLY VAL VAL THR ASP ASN GLY ASN VAL ILE LEU SEQRES 14 B 219 ASP VAL HIS GLY MSE GLU ILE LEU ASP PRO ILE ALA MSE SEQRES 15 B 219 GLU ASN ALA ILE ASN ALA ILE PRO GLY VAL VAL THR VAL SEQRES 16 B 219 GLY LEU PHE ALA ASN ARG GLY ALA ASP VAL ALA LEU ILE SEQRES 17 B 219 GLY THR PRO ASP GLY VAL LYS THR ILE VAL LYS MODRES 1O8B MSE A 90 MET SELENOMETHIONINE MODRES 1O8B MSE A 92 MET SELENOMETHIONINE MODRES 1O8B MSE A 138 MET SELENOMETHIONINE MODRES 1O8B MSE A 174 MET SELENOMETHIONINE MODRES 1O8B MSE A 182 MET SELENOMETHIONINE MODRES 1O8B MSE B 42 MET SELENOMETHIONINE MODRES 1O8B MSE B 90 MET SELENOMETHIONINE MODRES 1O8B MSE B 92 MET SELENOMETHIONINE MODRES 1O8B MSE B 138 MET SELENOMETHIONINE MODRES 1O8B MSE B 174 MET SELENOMETHIONINE MODRES 1O8B MSE B 182 MET SELENOMETHIONINE HET MSE A 90 8 HET MSE A 92 8 HET MSE A 138 8 HET MSE A 174 8 HET MSE A 182 8 HET MSE B 42 8 HET MSE B 90 8 HET MSE B 92 8 HET MSE B 138 8 HET MSE B 174 8 HET MSE B 182 8 HET ABF A1269 14 HET ABF B1269 14 HETNAM MSE SELENOMETHIONINE HETNAM ABF 5-O-PHOSPHONO-BETA-D-ARABINOFURANOSE HETSYN ABF BETA-D-ARABINOFURANOSE-5'-PHOSPHATE; 5-O-PHOSPHONO- HETSYN 2 ABF BETA-D-ARABINOSE; 5-O-PHOSPHONO-D-ARABINOSE; 5-O- HETSYN 3 ABF PHOSPHONO-ARABINOSE FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 3 ABF 2(C5 H11 O8 P) FORMUL 5 HOH *159(H2 O) HELIX 1 1 ASP A 69 VAL A 73 5 5 HELIX 2 2 LEU A 100 VAL A 109 1 10 HELIX 3 3 ALA A 139 LEU A 150 1 12 HELIX 4 4 PRO A 179 ALA A 188 1 10 HELIX 5 5 THR B 2 TYR B 17 1 16 HELIX 6 6 GLY B 29 THR B 41 1 13 HELIX 7 7 ASP B 54 LEU B 63 1 10 HELIX 8 8 ASP B 69 VAL B 73 5 5 HELIX 9 9 LEU B 100 VAL B 109 1 10 HELIX 10 10 ALA B 139 LEU B 150 1 12 HELIX 11 11 PRO B 179 ALA B 188 1 10 SHEET 1 AA 6 GLY A 48 SER A 52 0 SHEET 2 AA 6 VAL A 24 VAL A 26 1 O VAL A 24 N VAL A 50 SHEET 3 AA 6 GLY A 77 ASP A 81 1 O ILE A 78 N GLY A 25 SHEET 4 AA 6 LYS A 112 ILE A 116 1 N GLU A 111 O LEU A 76 SHEET 5 AA 6 VAL A 205 THR A 210 1 O VAL A 205 N CYS A 115 SHEET 6 AA 6 ASP A 212 VAL A 218 -1 O GLY A 213 N THR A 210 SHEET 1 AB 4 LYS A 121 VAL A 123 0 SHEET 2 AB 4 GLU A 85 ILE A 86 1 O ILE A 86 N VAL A 123 SHEET 3 AB 4 MSE A 90 LYS A 94 -1 N ILE A 93 O GLU A 85 SHEET 4 AB 4 GLY A 196 PHE A 198 -1 O PHE A 198 N MSE A 92 SHEET 1 AC 4 ARG A 153 TYR A 156 0 SHEET 2 AC 4 VAL A 167 HIS A 172 -1 O ASP A 170 N GLU A 155 SHEET 3 AC 4 LEU A 131 VAL A 135 -1 O LEU A 131 N VAL A 171 SHEET 4 AC 4 VAL A 192 VAL A 195 -1 N VAL A 193 O GLU A 134 SHEET 1 BA 7 HIS B 66 PHE B 68 0 SHEET 2 BA 7 GLY B 48 SER B 52 1 O ALA B 49 N PHE B 68 SHEET 3 BA 7 ILE B 23 VAL B 26 1 O VAL B 24 N VAL B 50 SHEET 4 BA 7 LEU B 76 ASP B 81 1 N GLY B 77 O ILE B 23 SHEET 5 BA 7 LYS B 112 ILE B 116 1 N GLU B 111 O LEU B 76 SHEET 6 BA 7 VAL B 205 THR B 210 1 O VAL B 205 N CYS B 115 SHEET 7 BA 7 ASP B 212 ILE B 217 -1 O GLY B 213 N THR B 210 SHEET 1 BB 4 LYS B 121 VAL B 123 0 SHEET 2 BB 4 GLU A 85 ILE A 86 1 O ILE A 86 N VAL A 123 SHEET 3 BB 4 MSE B 90 ILE B 93 -1 N ILE B 93 O GLU B 85 SHEET 4 BB 4 GLY B 196 PHE B 198 -1 O PHE B 198 N MSE B 92 SHEET 1 BC 4 ARG B 153 TYR B 156 0 SHEET 2 BC 4 VAL B 167 HIS B 172 -1 O ASP B 170 N GLU B 155 SHEET 3 BC 4 LEU B 131 VAL B 135 -1 O LEU B 131 N VAL B 171 SHEET 4 BC 4 VAL B 192 VAL B 195 -1 N VAL B 193 O GLU B 134 LINK C HIS A 89 N MSE A 90 1555 1555 1.34 LINK C MSE A 90 N GLN A 91 1555 1555 1.33 LINK C GLN A 91 N MSE A 92 1555 1555 1.32 LINK C MSE A 92 N ILE A 93 1555 1555 1.35 LINK C PRO A 137 N MSE A 138 1555 1555 1.33 LINK C MSE A 138 N ALA A 139 1555 1555 1.33 LINK C GLY A 173 N MSE A 174 1555 1555 1.32 LINK C MSE A 174 N GLU A 175 1555 1555 1.32 LINK C ALA A 181 N MSE A 182 1555 1555 1.33 LINK C MSE A 182 N GLU A 183 1555 1555 1.32 LINK C THR B 41 N MSE B 42 1555 1555 1.33 LINK C MSE B 42 N LYS B 43 1555 1555 1.33 LINK C HIS B 89 N MSE B 90 1555 1555 1.34 LINK C MSE B 90 N GLN B 91 1555 1555 1.33 LINK C GLN B 91 N MSE B 92 1555 1555 1.32 LINK C MSE B 92 N ILE B 93 1555 1555 1.34 LINK C PRO B 137 N MSE B 138 1555 1555 1.32 LINK C MSE B 138 N ALA B 139 1555 1555 1.33 LINK C GLY B 173 N MSE B 174 1555 1555 1.32 LINK C MSE B 174 N GLU B 175 1555 1555 1.33 LINK C ALA B 181 N MSE B 182 1555 1555 1.32 LINK C MSE B 182 N GLU B 183 1555 1555 1.33 CRYST1 42.049 42.400 60.195 90.23 100.98 98.98 P 1 2 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 0.023782 0.003758 0.004748 0.00000 SCALE2 0.000000 0.023878 0.000831 0.00000 SCALE3 0.000000 0.000000 0.016933 0.00000