HEADER OXIDOREDUCTASE 19-MAY-10 3N37 TITLE RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 SUBUNIT BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEOTIDE REDUCTASE 2, R2F PROTEIN; COMPND 5 EC: 1.17.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B2676, JW2651, NRDF, YGAD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBONUCLEOTIDE REDUCTASE, FOUR-HELIX BUNDLE, DIMANGANESE CLUSTER, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BOAL,J.A.COTRUVO JR.,J.STUBBE,A.C.ROSENZWEIG REVDAT 3 06-SEP-23 3N37 1 REMARK LINK REVDAT 2 24-NOV-10 3N37 1 JRNL REVDAT 1 18-AUG-10 3N37 0 JRNL AUTH A.K.BOAL,J.A.COTRUVO,J.STUBBE,A.C.ROSENZWEIG JRNL TITL STRUCTURAL BASIS FOR ACTIVATION OF CLASS IB RIBONUCLEOTIDE JRNL TITL 2 REDUCTASE. JRNL REF SCIENCE V. 329 1526 2010 JRNL REFN ISSN 0036-8075 JRNL PMID 20688982 JRNL DOI 10.1126/SCIENCE.1190187 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 57359 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2902 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3850 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2295 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.92000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : -1.38000 REMARK 3 B12 (A**2) : 0.46000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.571 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2473 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3390 ; 1.088 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 321 ; 4.318 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;41.833 ;25.207 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 434 ;13.055 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;17.763 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 374 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1907 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1484 ; 0.471 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2421 ; 0.953 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 989 ; 1.769 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 951 ; 3.013 ; 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 : 1 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 20.4162 26.4494 -10.7832 REMARK 3 T TENSOR REMARK 3 T11: 0.0696 T22: 0.0145 REMARK 3 T33: 0.0452 T12: -0.0109 REMARK 3 T13: 0.0296 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.8255 L22: 0.3519 REMARK 3 L33: 0.6823 L12: -0.0503 REMARK 3 L13: 0.2031 L23: 0.2200 REMARK 3 S TENSOR REMARK 3 S11: 0.0905 S12: -0.0428 S13: 0.0830 REMARK 3 S21: 0.0267 S22: -0.0492 S23: -0.0130 REMARK 3 S31: -0.0356 S32: -0.0388 S33: -0.0413 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3N37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059322. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 67.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 STARTING MODEL: 1R2F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 30% PEG 4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 177.83600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.91800 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 133.37700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.45900 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 222.29500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 177.83600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 88.91800 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 44.45900 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 133.37700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 222.29500 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: 3590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -44.45900 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 A 557 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 586 LIES ON A SPECIAL POSITION. 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 LYS A 2 REMARK 465 LEU A 3 REMARK 465 SER A 4 REMARK 465 ASN A 289 REMARK 465 ALA A 290 REMARK 465 ASP A 291 REMARK 465 GLU A 292 REMARK 465 ASN A 293 REMARK 465 HIS A 294 REMARK 465 ASP A 295 REMARK 465 PHE A 296 REMARK 465 PHE A 297 REMARK 465 SER A 298 REMARK 465 GLY A 299 REMARK 465 SER A 300 REMARK 465 GLY A 301 REMARK 465 SER A 302 REMARK 465 SER A 303 REMARK 465 TYR A 304 REMARK 465 VAL A 305 REMARK 465 MET A 306 REMARK 465 GLY A 307 REMARK 465 LYS A 308 REMARK 465 ALA A 309 REMARK 465 VAL A 310 REMARK 465 GLU A 311 REMARK 465 THR A 312 REMARK 465 GLU A 313 REMARK 465 ASP A 314 REMARK 465 GLU A 315 REMARK 465 ASP A 316 REMARK 465 TRP A 317 REMARK 465 ASN A 318 REMARK 465 PHE A 319 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 543 O HOH A 574 1.86 REMARK 500 O HOH A 559 O HOH A 574 1.98 REMARK 500 O HOH A 538 O HOH A 614 2.15 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 394 O HOH A 580 12554 2.00 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 PHE A 160 -69.90 -138.73 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 320 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 67 OD1 REMARK 620 2 GLU A 98 OE1 90.0 REMARK 620 3 HIS A 101 ND1 103.6 93.8 REMARK 620 4 GLU A 158 OE1 91.0 104.4 156.7 REMARK 620 5 GLU A 192 OE2 168.9 86.9 87.2 79.4 REMARK 620 6 HOH A 401 O 83.8 173.2 90.4 73.1 98.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 321 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 98 OE2 REMARK 620 2 GLU A 158 OE2 90.8 REMARK 620 3 GLU A 192 OE1 161.8 84.7 REMARK 620 4 GLU A 192 OE2 104.4 90.1 58.1 REMARK 620 5 HIS A 195 ND1 95.3 173.3 88.6 85.7 REMARK 620 6 HOH A 688 O 96.2 87.8 101.2 159.4 94.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 322 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N38 RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE NRDF FROM ESCHERICHIA COLI SOAKED WITH REMARK 900 FERROUS IONS REMARK 900 RELATED ID: 3N39 RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI REMARK 900 IN COMPLEX WITH NRDI REMARK 900 RELATED ID: 3N3A RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI REMARK 900 IN COMPLEX WITH REDUCED NRDI REMARK 900 RELATED ID: 3N3B RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ACTIVATION OF CLASS IB RIBONUCLEOTIDE REDUCTASE DBREF 3N37 A 1 319 UNP P37146 RIR4_ECOLI 1 319 SEQRES 1 A 319 MET LYS LEU SER ARG ILE SER ALA ILE ASN TRP ASN LYS SEQRES 2 A 319 ILE SER ASP ASP LYS ASP LEU GLU VAL TRP ASN ARG LEU SEQRES 3 A 319 THR SER ASN PHE TRP LEU PRO GLU LYS VAL PRO LEU SER SEQRES 4 A 319 ASN ASP ILE PRO ALA TRP GLN THR LEU THR VAL VAL GLU SEQRES 5 A 319 GLN GLN LEU THR MET ARG VAL PHE THR GLY LEU THR LEU SEQRES 6 A 319 LEU ASP THR LEU GLN ASN VAL ILE GLY ALA PRO SER LEU SEQRES 7 A 319 MET PRO ASP ALA LEU THR PRO HIS GLU GLU ALA VAL LEU SEQRES 8 A 319 SER ASN ILE SER PHE MET GLU ALA VAL HIS ALA ARG SER SEQRES 9 A 319 TYR SER SER ILE PHE SER THR LEU CYS GLN THR LYS ASP SEQRES 10 A 319 VAL ASP ALA ALA TYR ALA TRP SER GLU GLU ASN ALA PRO SEQRES 11 A 319 LEU GLN ARG LYS ALA GLN ILE ILE GLN GLN HIS TYR ARG SEQRES 12 A 319 GLY ASP ASP PRO LEU LYS LYS LYS ILE ALA SER VAL PHE SEQRES 13 A 319 LEU GLU SER PHE LEU PHE TYR SER GLY PHE TRP LEU PRO SEQRES 14 A 319 MET TYR PHE SER SER ARG GLY LYS LEU THR ASN THR ALA SEQRES 15 A 319 ASP LEU ILE ARG LEU ILE ILE ARG ASP GLU ALA VAL HIS SEQRES 16 A 319 GLY TYR TYR ILE GLY TYR LYS TYR GLN LYS ASN MET GLU SEQRES 17 A 319 LYS ILE SER LEU GLY GLN ARG GLU GLU LEU LYS SER PHE SEQRES 18 A 319 ALA PHE ASP LEU LEU LEU GLU LEU TYR ASP ASN GLU LEU SEQRES 19 A 319 GLN TYR THR ASP GLU LEU TYR ALA GLU THR PRO TRP ALA SEQRES 20 A 319 ASP ASP VAL LYS ALA PHE LEU CYS TYR ASN ALA ASN LYS SEQRES 21 A 319 ALA LEU MET ASN LEU GLY TYR GLU PRO LEU PHE PRO ALA SEQRES 22 A 319 GLU MET ALA GLU VAL ASN PRO ALA ILE LEU ALA ALA LEU SEQRES 23 A 319 SER PRO ASN ALA ASP GLU ASN HIS ASP PHE PHE SER GLY SEQRES 24 A 319 SER GLY SER SER TYR VAL MET GLY LYS ALA VAL GLU THR SEQRES 25 A 319 GLU ASP GLU ASP TRP ASN PHE HET MN A 320 1 HET MN A 321 1 HET GOL A 322 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 C3 H8 O3 FORMUL 5 HOH *400(H2 O) HELIX 1 1 ASP A 16 ASN A 29 1 14 HELIX 2 2 LEU A 32 VAL A 36 5 5 HELIX 3 3 PRO A 37 ASN A 40 5 4 HELIX 4 4 ASP A 41 GLN A 46 1 6 HELIX 5 5 THR A 49 ILE A 73 1 25 HELIX 6 6 ILE A 73 MET A 79 1 7 HELIX 7 7 PRO A 80 ALA A 82 5 3 HELIX 8 8 THR A 84 CYS A 113 1 30 HELIX 9 9 GLN A 114 ASN A 128 1 15 HELIX 10 10 ASN A 128 GLY A 144 1 17 HELIX 11 11 ASP A 146 PHE A 160 1 15 HELIX 12 12 PHE A 162 ARG A 175 1 14 HELIX 13 13 LEU A 178 GLU A 208 1 31 HELIX 14 14 SER A 211 TYR A 241 1 31 HELIX 15 15 TRP A 246 LEU A 265 1 20 HELIX 16 16 PRO A 272 ALA A 276 5 5 HELIX 17 17 ASN A 279 SER A 287 1 9 LINK OD1 ASP A 67 MN MN A 320 1555 1555 2.08 LINK OE1 GLU A 98 MN MN A 320 1555 1555 2.13 LINK OE2 GLU A 98 MN MN A 321 1555 1555 2.14 LINK ND1 HIS A 101 MN MN A 320 1555 1555 2.34 LINK OE1 GLU A 158 MN MN A 320 1555 1555 2.24 LINK OE2 GLU A 158 MN MN A 321 1555 1555 2.15 LINK OE2 GLU A 192 MN MN A 320 1555 1555 2.24 LINK OE1 GLU A 192 MN MN A 321 1555 1555 2.21 LINK OE2 GLU A 192 MN MN A 321 1555 1555 2.33 LINK ND1 HIS A 195 MN MN A 321 1555 1555 2.31 LINK MN MN A 320 O HOH A 401 1555 1555 2.30 LINK MN MN A 321 O HOH A 688 1555 1555 2.06 SITE 1 AC1 6 ASP A 67 GLU A 98 HIS A 101 GLU A 158 SITE 2 AC1 6 GLU A 192 HOH A 401 SITE 1 AC2 5 GLU A 98 GLU A 158 GLU A 192 HIS A 195 SITE 2 AC2 5 HOH A 688 SITE 1 AC3 4 GLN A 46 PRO A 269 LEU A 270 PRO A 272 CRYST1 78.142 78.142 266.754 90.00 90.00 120.00 P 65 2 2 12 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 0.012797 0.007388 0.000000 0.00000 SCALE2 0.000000 0.014777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003749 0.00000