HEADER OXIDOREDUCTASE 22-MAY-03 1PEM TITLE RIBONUCLEOTIDE REDUCTASE PROTEIN R1E FROM SALMONELLA TYPHIMURIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEOTIDE REDUCTASE 2, R1E PROTEIN; COMPND 5 EC: 1.17.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 GENE: NRDE OR STM2807; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS 10 STRANDED ALPHA/BETA BARREL, PROTEIN-SPECIFICITY-EFFECTOR COMPLEX, KEYWDS 2 DATP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.UPPSTEN,M.FARNEGARDH,A.JORDAN,R.ELIASSON,H.EKLUND,U.UHLIN REVDAT 4 03-APR-24 1PEM 1 REMARK REVDAT 3 14-FEB-24 1PEM 1 REMARK REVDAT 2 24-FEB-09 1PEM 1 VERSN REVDAT 1 25-MAY-04 1PEM 0 JRNL AUTH M.UPPSTEN,M.FARNEGARDH,A.JORDAN,R.ELIASSON,H.EKLUND,U.UHLIN JRNL TITL STRUCTURE OF THE LARGE SUBUNIT OF CLASS IB RIBONUCLEOTIDE JRNL TITL 2 REDUCTASE FROM SALMONELLA TYPHIMURIUM AND ITS COMPLEXES WITH JRNL TITL 3 ALLOSTERIC EFFECTORS. JRNL REF J.MOL.BIOL. V. 330 87 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12818204 JRNL DOI 10.1016/S0022-2836(03)00538-2 REMARK 2 REMARK 2 RESOLUTION. 2.99 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 20.0 REMARK 3 NUMBER OF REFLECTIONS : 28433 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1518 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) : 2.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2019 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5447 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.04000 REMARK 3 B22 (A**2) : -1.04000 REMARK 3 B33 (A**2) : 2.08000 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): 0.601 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.325 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.349 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.076 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5573 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4993 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7545 ; 1.770 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11551 ; 0.884 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 680 ; 3.820 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 977 ;19.818 ;15.000 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): 818 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6274 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1233 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1482 ; 0.273 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5568 ; 0.251 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 4 ; 0.061 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 250 ; 0.148 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 3 ; 0.111 ; 0.500 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 ; 0.221 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 66 ; 0.332 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.143 ; 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): 3389 ; 0.673 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5444 ; 1.279 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2184 ; 1.232 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2101 ; 2.303 ; 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 : 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 : 1.40 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 1PEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL,SI(111) OR REMARK 200 SI(311) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30043 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : 0.11400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : 0.42000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.600 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: POLY-ALANIN MODEL OF RIBONUCLEOTIDE REDUCTASE REMARK 200 PROTEIN R1 FROM E.COLI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE, MAGNESIUM CHLORIDE, REMARK 280 DTT, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 145.14250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.53950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.53950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 217.71375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.53950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.53950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.57125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.53950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.53950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 217.71375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.53950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.53950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.57125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 145.14250 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: THE BIOLOGICAL HOMODIMER IS REMARK 300 GENERATED BY THE TWO FOLD AXIS: REMARK 300 -Y, -X, -Z+1/2 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 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 290.28500 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 GLU A 7 REMARK 465 ARG A 8 REMARK 465 VAL A 9 REMARK 465 MET A 10 REMARK 465 GLN A 11 REMARK 465 GLU A 12 REMARK 465 GLN A 247 REMARK 465 LEU A 248 REMARK 465 GLY A 249 REMARK 465 ALA A 250 REMARK 465 ARG A 251 REMARK 465 ALA A 700 REMARK 465 LEU A 701 REMARK 465 GLU A 702 REMARK 465 GLY A 703 REMARK 465 THR A 704 REMARK 465 GLU A 705 REMARK 465 ILE A 706 REMARK 465 GLU A 707 REMARK 465 GLY A 708 REMARK 465 CYS A 709 REMARK 465 VAL A 710 REMARK 465 SER A 711 REMARK 465 CYS A 712 REMARK 465 ALA A 713 REMARK 465 LEU A 714 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 15 N ASP A 15 CA 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 ASP A 15 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 ASP A 128 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 185 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 240 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 540 CB - CA - C ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP A 540 N - CA - C ANGL. DEV. = -21.2 DEGREES REMARK 500 ASP A 540 CA - C - N ANGL. DEV. = 22.2 DEGREES REMARK 500 ASP A 540 O - C - N ANGL. DEV. = -12.0 DEGREES REMARK 500 ASP A 541 C - N - CA ANGL. DEV. = 23.2 DEGREES REMARK 500 ASP A 541 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP A 542 CA - CB - CG ANGL. DEV. = -15.5 DEGREES REMARK 500 ASP A 637 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 675 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ILE A 694 N - CA - C ANGL. DEV. = -16.6 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 MET A 14 17.35 -57.02 REMARK 500 LYS A 28 -13.20 -45.76 REMARK 500 GLN A 33 50.46 87.75 REMARK 500 HIS A 48 -50.30 -128.72 REMARK 500 ALA A 78 5.52 -67.80 REMARK 500 SER A 111 2.54 -152.80 REMARK 500 LYS A 120 -3.39 -142.82 REMARK 500 GLN A 139 47.26 36.77 REMARK 500 SER A 177 44.98 -141.81 REMARK 500 LYS A 202 9.50 -53.20 REMARK 500 ARG A 203 68.22 -165.49 REMARK 500 ARG A 223 -9.44 78.27 REMARK 500 SER A 228 120.94 179.97 REMARK 500 ALA A 245 32.95 -69.92 REMARK 500 LYS A 273 33.86 -99.88 REMARK 500 ASP A 278 -171.19 -69.02 REMARK 500 GLU A 302 31.80 -93.70 REMARK 500 ASN A 303 42.58 37.48 REMARK 500 LYS A 518 149.08 -171.44 REMARK 500 ALA A 585 134.19 -176.48 REMARK 500 HIS A 597 67.55 64.51 REMARK 500 SER A 600 92.19 -60.70 REMARK 500 SER A 601 -168.36 69.58 REMARK 500 ILE A 602 40.06 -83.85 REMARK 500 PHE A 626 13.10 57.78 REMARK 500 ASN A 629 0.10 -60.33 REMARK 500 ASN A 631 16.10 -143.97 REMARK 500 TYR A 635 76.58 -105.60 REMARK 500 GLN A 659 -69.15 -96.28 REMARK 500 TYR A 692 -75.29 -103.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 14 ASP A 15 142.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2R1R RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH DTTP OCCUPYING THE REMARK 900 SPECIFICITY SITE FROM ESCHERICHIA COLI REMARK 900 RELATED ID: 1R1R RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R1 PROTEIN MUTANT Y730F WITH A REDUCED REMARK 900 ACTIVE SITE FROM ESCHERICHIA COLI REMARK 900 RELATED ID: 1PEO RELATED DB: PDB REMARK 900 STRUCTURE OF THE LARGE SUBUNIT OF CLASS IB RIBONUCLEOTIDE REDUCTASE REMARK 900 FROM SALMONELLA TYPHIMURIUM AND ITS COMPLEXES WITH ALLOSTERIC REMARK 900 EFFECTORS REMARK 900 RELATED ID: 1PEQ RELATED DB: PDB REMARK 900 STRUCTURE OF THE LARGE SUBUNIT OF CLASS IB RIBONUCLEOTIDE REDUCTASE REMARK 900 FROM SALMONELLA TYPHIMURIUM AND ITS COMPLEXES WITH ALLOSTERIC REMARK 900 EFFECTORS REMARK 900 RELATED ID: 1PEU RELATED DB: PDB REMARK 900 STRUCTURE OF THE LARGE SUBUNIT OF CLASS IB RIBONUCLEOTIDE REDUCTASE REMARK 900 FROM SALMONELLA TYPHIMURIUM AND ITS COMPLEXES WITH ALLOSTERIC REMARK 900 EFFECTORS DBREF 1PEM A 1 714 UNP Q08698 RIR3_SALTY 0 713 SEQRES 1 A 714 MET ALA THR THR THR PRO GLU ARG VAL MET GLN GLU THR SEQRES 2 A 714 MET ASP TYR HIS ALA LEU ASN ALA MET LEU ASN LEU TYR SEQRES 3 A 714 ASP LYS ALA GLY HIS ILE GLN PHE ASP LYS ASP GLN GLN SEQRES 4 A 714 ALA ILE ASP ALA PHE PHE ALA THR HIS VAL ARG PRO HIS SEQRES 5 A 714 SER VAL THR PHE ALA SER GLN HIS GLU ARG LEU GLY THR SEQRES 6 A 714 LEU VAL ARG GLU GLY TYR TYR ASP ASP ALA VAL LEU ALA SEQRES 7 A 714 ARG TYR ASP ARG ALA PHE VAL LEU ARG LEU PHE GLU HIS SEQRES 8 A 714 ALA HIS ALA SER GLY PHE ARG PHE GLN THR PHE LEU GLY SEQRES 9 A 714 ALA TRP LYS PHE TYR THR SER TYR THR LEU LYS THR PHE SEQRES 10 A 714 ASP GLY LYS ARG TYR LEU GLU HIS PHE GLU ASP ARG VAL SEQRES 11 A 714 THR MET VAL ALA LEU THR LEU ALA GLN GLY ASP GLU THR SEQRES 12 A 714 LEU ALA THR GLN LEU THR ASP GLU MET LEU SER GLY ARG SEQRES 13 A 714 PHE GLN PRO ALA THR PRO THR PHE LEU ASN CYS GLY LYS SEQRES 14 A 714 GLN GLN ARG GLY GLU LEU VAL SER CYS PHE LEU LEU ARG SEQRES 15 A 714 ILE GLU ASP ASN MET GLU SER ILE GLY ARG ALA VAL ASN SEQRES 16 A 714 SER ALA LEU GLN LEU SER LYS ARG GLY GLY GLY VAL ALA SEQRES 17 A 714 PHE LEU LEU SER ASN LEU ARG GLU ALA GLY ALA PRO ILE SEQRES 18 A 714 LYS ARG ILE GLU ASN GLN SER SER GLY VAL ILE PRO VAL SEQRES 19 A 714 MET LYS MET LEU GLU ASP ALA PHE SER TYR ALA ASN GLN SEQRES 20 A 714 LEU GLY ALA ARG GLN GLY ALA GLY ALA VAL TYR LEU HIS SEQRES 21 A 714 ALA HIS HIS PRO ASP ILE LEU ARG PHE LEU ASP THR LYS SEQRES 22 A 714 ARG GLU ASN ALA ASP GLU LYS ILE ARG ILE LYS THR LEU SEQRES 23 A 714 SER LEU GLY VAL VAL ILE PRO ASP ILE THR PHE ARG LEU SEQRES 24 A 714 ALA LYS GLU ASN ALA GLN MET ALA LEU PHE SER PRO TYR SEQRES 25 A 714 ASP ILE GLN ARG ARG TYR GLY LYS PRO PHE GLY ASP ILE SEQRES 26 A 714 ALA ILE SER GLU ARG TYR ASP GLU LEU ILE ALA ASP PRO SEQRES 27 A 714 HIS VAL ARG LYS THR TYR ILE ASN ALA ARG ASP PHE PHE SEQRES 28 A 714 GLN THR LEU ALA GLU ILE GLN PHE GLU SER GLY TYR PRO SEQRES 29 A 714 TYR ILE MET PHE GLU ASP THR VAL ASN ARG ALA ASN PRO SEQRES 30 A 714 ILE ALA GLY ARG ILE ASN MET SER ASN LEU CYS SER GLU SEQRES 31 A 714 ILE LEU GLN VAL ASN SER ALA SER ARG TYR ASP ASP ASN SEQRES 32 A 714 LEU ASP TYR THR HIS ILE GLY HIS ASP ILE SER CYS ASN SEQRES 33 A 714 LEU GLY SER LEU ASN ILE ALA HIS VAL MET ASP SER PRO SEQRES 34 A 714 ASP ILE GLY ARG THR VAL GLU THR ALA ILE ARG GLY LEU SEQRES 35 A 714 THR ALA VAL SER ASP MET SER HIS ILE ARG SER VAL PRO SEQRES 36 A 714 SER ILE ALA ALA GLY ASN ALA ALA SER HIS ALA ILE GLY SEQRES 37 A 714 LEU GLY GLN MET ASN LEU HIS GLY TYR LEU ALA ARG GLU SEQRES 38 A 714 GLY ILE ALA TYR GLY SER PRO GLU ALA LEU ASP PHE THR SEQRES 39 A 714 ASN LEU TYR PHE TYR THR ILE THR TRP HIS ALA VAL HIS SEQRES 40 A 714 THR SER MET ARG LEU ALA ARG GLU ARG GLY LYS THR PHE SEQRES 41 A 714 ALA GLY PHE ALA GLN SER ARG TYR ALA SER GLY ASP TYR SEQRES 42 A 714 PHE THR GLN TYR LEU GLN ASP ASP TRP GLN PRO LYS THR SEQRES 43 A 714 ALA LYS VAL ARG ALA LEU PHE ALA ARG SER GLY ILE THR SEQRES 44 A 714 LEU PRO THR ARG GLU MET TRP LEU LYS LEU ARG ASP ASP SEQRES 45 A 714 VAL MET ARG TYR GLY ILE TYR ASN GLN ASN LEU GLN ALA SEQRES 46 A 714 VAL PRO PRO THR GLY SER ILE SER TYR ILE ASN HIS ALA SEQRES 47 A 714 THR SER SER ILE HIS PRO ILE VAL ALA LYS ILE GLU ILE SEQRES 48 A 714 ARG LYS GLU GLY LYS THR GLY ARG VAL TYR TYR PRO ALA SEQRES 49 A 714 PRO PHE MET THR ASN GLU ASN LEU ASP MET TYR GLN ASP SEQRES 50 A 714 ALA TYR ASP ILE GLY PRO GLU LYS ILE ILE ASP THR TYR SEQRES 51 A 714 ALA GLU ALA THR ARG HIS VAL ASP GLN GLY LEU SER LEU SEQRES 52 A 714 THR LEU PHE PHE PRO ASP THR ALA THR THR ARG ASP ILE SEQRES 53 A 714 ASN LYS ALA GLN ILE TYR ALA TRP ARG LYS GLY ILE LYS SEQRES 54 A 714 SER LEU TYR TYR ILE ARG LEU ARG GLN LEU ALA LEU GLU SEQRES 55 A 714 GLY THR GLU ILE GLU GLY CYS VAL SER CYS ALA LEU HELIX 1 1 ASP A 15 MET A 22 1 8 HELIX 2 2 LEU A 23 LEU A 25 5 3 HELIX 3 3 PHE A 34 HIS A 48 1 15 HELIX 4 4 HIS A 48 SER A 53 1 6 HELIX 5 5 SER A 58 GLU A 69 1 12 HELIX 6 6 ASP A 73 ALA A 78 1 6 HELIX 7 7 ASP A 81 ALA A 94 1 14 HELIX 8 8 THR A 101 TYR A 112 1 12 HELIX 9 9 HIS A 125 GLN A 139 1 15 HELIX 10 10 ASP A 141 SER A 154 1 14 HELIX 11 11 ALA A 160 CYS A 167 1 8 HELIX 12 12 ASN A 186 LYS A 202 1 17 HELIX 13 13 VAL A 231 ALA A 245 1 15 HELIX 14 14 ASP A 265 THR A 272 1 8 HELIX 15 15 ASP A 294 GLU A 302 1 9 HELIX 16 16 SER A 310 GLY A 319 1 10 HELIX 17 17 PRO A 321 ILE A 325 5 5 HELIX 18 18 ARG A 330 ASP A 337 1 8 HELIX 19 19 ALA A 347 GLY A 362 1 16 HELIX 20 20 PHE A 368 ASN A 376 1 9 HELIX 21 21 ILE A 422 ASP A 427 1 6 HELIX 22 22 ASP A 430 SER A 449 1 20 HELIX 23 23 VAL A 454 HIS A 465 1 12 HELIX 24 24 ASN A 473 GLU A 481 1 9 HELIX 25 25 SER A 487 GLY A 517 1 31 HELIX 26 26 GLY A 522 GLN A 525 5 4 HELIX 27 27 SER A 526 GLY A 531 1 6 HELIX 28 28 GLY A 531 GLN A 539 1 9 HELIX 29 29 ALA A 547 GLY A 557 1 11 HELIX 30 30 THR A 562 GLY A 577 1 16 HELIX 31 31 SER A 591 HIS A 597 1 7 HELIX 32 32 ASN A 631 TYR A 635 5 5 HELIX 33 33 ASP A 637 ARG A 655 1 19 HELIX 34 34 THR A 672 GLY A 687 1 16 SHEET 1 A 3 PHE A 157 PRO A 159 0 SHEET 2 A 3 ASN A 416 ASN A 421 -1 O SER A 419 N GLN A 158 SHEET 3 A 3 ILE A 467 MET A 472 1 O GLY A 470 N GLY A 418 SHEET 1 B 7 ILE A 413 SER A 414 0 SHEET 2 B 7 PHE A 179 LEU A 181 -1 N LEU A 180 O ILE A 413 SHEET 3 B 7 VAL A 207 LEU A 210 1 O ALA A 208 N LEU A 181 SHEET 4 B 7 GLY A 255 HIS A 260 1 O ALA A 256 N PHE A 209 SHEET 5 B 7 SER A 287 VAL A 291 1 O SER A 287 N VAL A 257 SHEET 6 B 7 TYR A 365 MET A 367 1 O TYR A 365 N VAL A 290 SHEET 7 B 7 SER A 690 LEU A 691 -1 O LEU A 691 N ILE A 366 SHEET 1 C 2 GLN A 305 PHE A 309 0 SHEET 2 C 2 LYS A 342 ASN A 346 -1 O ILE A 345 N MET A 306 SHEET 1 D 2 ARG A 399 TYR A 400 0 SHEET 2 D 2 TYR A 406 HIS A 408 -1 O THR A 407 N ARG A 399 SHEET 1 E 2 ILE A 609 ARG A 612 0 SHEET 2 E 2 VAL A 620 PRO A 623 -1 O VAL A 620 N ARG A 612 SHEET 1 F 2 LEU A 665 PHE A 666 0 SHEET 2 F 2 ILE A 694 ARG A 695 1 O ARG A 695 N LEU A 665 CISPEP 1 TYR A 363 PRO A 364 0 -5.56 CISPEP 2 ASP A 540 ASP A 541 0 17.77 CRYST1 99.079 99.079 290.285 90.00 90.00 90.00 P 43 21 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 0.010093 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003445 0.00000