HEADER OXIDOREDUCTASE 22-MAY-03 1PEO 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 DCTP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.UPPSTEN,M.FARNEGARDH,A.JORDAN,R.ELIASSON,H.EKLUND,U.UHLIN REVDAT 4 06-NOV-24 1PEO 1 REMARK REVDAT 3 03-APR-24 1PEO 1 REMARK REVDAT 2 24-FEB-09 1PEO 1 VERSN REVDAT 1 25-MAY-04 1PEO 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. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28258 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1508 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1997 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5436 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 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) : 37.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60000 REMARK 3 B22 (A**2) : -0.60000 REMARK 3 B33 (A**2) : 1.20000 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): 0.590 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.340 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.338 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.582 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5627 ; 0.029 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 5039 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7623 ; 2.359 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11651 ; 0.992 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 683 ; 5.011 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 985 ;20.927 ;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): 824 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6310 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1248 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1773 ; 0.305 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5859 ; 0.258 ; 0.300 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): 356 ; 0.184 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 14 ; 0.127 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.066 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 26 ; 0.198 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 86 ; 0.262 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.119 ; 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): 3402 ; 1.014 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5464 ; 1.945 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2225 ; 2.798 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2159 ; 4.910 ; 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 1PEO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-02 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 : ID14-1 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 : DIAMOND (111), GE(220) REMARK 200 OPTICS : NULL 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 : 28924 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.35 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : 0.45000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 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 (%): 71.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.38 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 144.57550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.46900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.46900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 216.86325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.46900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.46900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.28775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.46900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.46900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 216.86325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.46900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.46900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.28775 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 144.57550 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 289.15100 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 275 REMARK 465 ASN A 276 REMARK 465 ALA A 277 REMARK 465 ASP A 278 REMARK 465 GLU A 279 REMARK 465 LYS A 280 REMARK 465 ILE A 281 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 274 O 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 ILE A 605 N ALA A 607 1.88 REMARK 500 NZ LYS A 608 O TYR A 635 1.98 REMARK 500 O GLU A 302 N ALA A 304 2.15 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 GLU A 12 N - CA - C ANGL. DEV. = 18.5 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 73 CB - CG - OD2 ANGL. DEV. = 8.7 DEGREES REMARK 500 ASP A 74 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 182 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 192 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 192 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 215 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 215 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 240 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP A 332 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 337 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 349 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 427 CB - CG - OD2 ANGL. DEV. = 9.1 DEGREES REMARK 500 ASP A 541 CA - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 ASP A 669 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 LEU A 696 CA - CB - CG ANGL. DEV. = -17.3 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 LYS A 28 -17.11 -43.71 REMARK 500 GLN A 33 65.23 -69.17 REMARK 500 HIS A 48 -48.35 -131.71 REMARK 500 VAL A 49 -77.54 -71.97 REMARK 500 ALA A 78 0.33 -67.50 REMARK 500 VAL A 85 -97.91 -54.07 REMARK 500 LEU A 86 -47.70 -11.79 REMARK 500 ALA A 105 -71.23 -41.85 REMARK 500 SER A 177 17.73 -151.01 REMARK 500 ARG A 223 15.29 58.99 REMARK 500 ASN A 226 71.50 35.44 REMARK 500 ASN A 246 -171.47 -65.41 REMARK 500 ASN A 303 65.72 -11.78 REMARK 500 SER A 361 15.86 -143.80 REMARK 500 PHE A 368 70.59 -68.49 REMARK 500 GLU A 369 -51.42 -29.50 REMARK 500 SER A 389 15.44 54.57 REMARK 500 LEU A 404 -1.86 90.58 REMARK 500 SER A 487 161.21 -47.13 REMARK 500 PHE A 523 -55.18 -29.67 REMARK 500 GLN A 539 -129.07 -98.88 REMARK 500 ASP A 541 -65.42 -131.09 REMARK 500 TRP A 542 -0.45 -9.75 REMARK 500 ALA A 585 139.58 -171.37 REMARK 500 SER A 600 -24.95 -28.09 REMARK 500 SER A 601 -73.53 -178.97 REMARK 500 ILE A 602 5.38 -157.26 REMARK 500 VAL A 606 -33.74 -20.40 REMARK 500 PHE A 626 14.81 57.37 REMARK 500 ASN A 631 20.05 -140.21 REMARK 500 ASP A 633 3.09 -66.03 REMARK 500 TYR A 635 67.66 -113.54 REMARK 500 TYR A 639 -73.57 -53.97 REMARK 500 GLN A 659 -120.91 -94.09 REMARK 500 TYR A 692 -131.07 -97.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR A 363 -10.01 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 MG A 715 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DCP A 716 O1G REMARK 620 2 DCP A 716 O2A 118.5 REMARK 620 3 DCP A 716 O1B 58.9 67.2 REMARK 620 4 DCP A 716 O3G 56.0 99.8 90.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 715 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A 716 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: 1PEM 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 1PEO 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 HET MG A 715 1 HET DCP A 716 28 HETNAM MG MAGNESIUM ION HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 DCP C9 H16 N3 O13 P3 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 GLN A 33 HIS A 48 1 16 HELIX 4 4 VAL A 49 SER A 53 5 5 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 HIS A 93 1 13 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 GLY A 155 1 15 HELIX 11 11 ALA A 160 CYS A 167 1 8 HELIX 12 12 ASN A 186 ARG A 203 1 18 HELIX 13 13 VAL A 231 ALA A 245 1 15 HELIX 14 14 ASP A 265 ASP A 271 1 7 HELIX 15 15 THR A 272 ARG A 274 5 3 HELIX 16 16 PRO A 293 GLU A 302 1 10 HELIX 17 17 SER A 310 GLY A 319 1 10 HELIX 18 18 PRO A 321 ILE A 325 5 5 HELIX 19 19 ALA A 326 ASP A 337 1 12 HELIX 20 20 ALA A 347 GLY A 362 1 16 HELIX 21 21 PHE A 368 ASN A 376 1 9 HELIX 22 22 ILE A 422 ASP A 427 1 6 HELIX 23 23 ASP A 430 MET A 448 1 19 HELIX 24 24 VAL A 454 HIS A 465 1 12 HELIX 25 25 ASN A 473 GLU A 481 1 9 HELIX 26 26 SER A 487 GLY A 517 1 31 HELIX 27 27 GLY A 522 GLN A 525 5 4 HELIX 28 28 SER A 526 GLY A 531 1 6 HELIX 29 29 ASP A 532 GLN A 539 5 8 HELIX 30 30 THR A 546 GLY A 557 1 12 HELIX 31 31 THR A 562 GLY A 577 1 16 HELIX 32 32 SER A 591 HIS A 597 1 7 HELIX 33 33 ASN A 631 TYR A 635 5 5 HELIX 34 34 ASP A 637 GLY A 642 1 6 HELIX 35 35 GLY A 642 ARG A 655 1 14 HELIX 36 36 THR A 672 LYS A 686 1 15 SHEET 1 A 3 PHE A 157 PRO A 159 0 SHEET 2 A 3 LEU A 417 ASN A 421 -1 O SER A 419 N GLN A 158 SHEET 3 A 3 GLY A 468 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 CYS A 178 LEU A 181 -1 N LEU A 180 O ILE A 413 SHEET 3 B 7 GLY A 206 LEU A 210 1 O ALA A 208 N LEU A 181 SHEET 4 B 7 GLY A 255 HIS A 260 1 O TYR A 258 N PHE A 209 SHEET 5 B 7 SER A 287 VAL A 291 1 O VAL A 291 N LEU A 259 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 HIS A 408 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 667 0 SHEET 2 F 2 ILE A 694 LEU A 696 1 O ARG A 695 N PHE A 667 SSBOND 1 CYS A 178 CYS A 415 1555 1555 2.09 LINK MG MG A 715 O1G DCP A 716 1555 1555 2.94 LINK MG MG A 715 O2A DCP A 716 1555 1555 2.15 LINK MG MG A 715 O1B DCP A 716 1555 1555 2.18 LINK MG MG A 715 O3G DCP A 716 1555 1555 2.22 CISPEP 1 TYR A 363 PRO A 364 0 -0.88 SITE 1 AC1 1 DCP A 716 SITE 1 AC2 10 ASP A 185 ASN A 186 MET A 187 LYS A 202 SITE 2 AC2 10 ARG A 215 ILE A 221 LYS A 222 TYR A 244 SITE 3 AC2 10 ASN A 246 MG A 715 CRYST1 98.938 98.938 289.151 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 0.010107 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003458 0.00000