HEADER OXIDOREDUCTASE 30-MAY-03 1PJ0 TITLE RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F MUTANT SOAKED WITH FERROUS IONS TITLE 2 AT NEUTRAL PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RIBONUCLEOTIDE REDUCTASE 1, B2 PROTEIN, R2 PROTEIN; COMPND 5 EC: 1.17.4.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: RIR2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FOUR HELIX BUNDLE, DIFERROUS CLUSTER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.C.VOEGTLI,M.SOMMERHALTER,L.SALEH,J.BALDWIN,J.M.BOLLINGER JR., AUTHOR 2 A.C.ROSENZWEIG REVDAT 6 20-NOV-24 1PJ0 1 REMARK REVDAT 5 16-AUG-23 1PJ0 1 REMARK REVDAT 4 27-OCT-21 1PJ0 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1PJ0 1 VERSN REVDAT 2 24-FEB-09 1PJ0 1 VERSN REVDAT 1 13-JAN-04 1PJ0 0 JRNL AUTH W.C.VOEGTLI,M.SOMMERHALTER,L.SALEH,J.BALDWIN, JRNL AUTH 2 J.M.BOLLINGER JR.,A.C.ROSENZWEIG JRNL TITL VARIABLE COORDINATION GEOMETRIES AT THE DIIRON(II) ACTIVE JRNL TITL 2 SITE OF RIBONUCLEOTIDE REDUCTASE R2. JRNL REF J.AM.CHEM.SOC. V. 125 15822 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 14677973 JRNL DOI 10.1021/JA0370387 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 592822.390 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 54370 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 SET) : 0.204 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2736 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7344 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 403 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5562 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 254 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.39000 REMARK 3 B22 (A**2) : 3.19000 REMARK 3 B33 (A**2) : 0.20000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.630 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.080 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.960 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 47.76 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : TOPPER_ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : TOPPER_ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54370 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1PIM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 200MM NACL, 50MM MES, REMARK 280 0.3% DIOXANE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 37.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.20000 REMARK 290 SMTRY3 4 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 300 REMARK: TETRAMER OF TWO ALPHA AND TWO BETA SUBUNITS 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -238.0 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 SER A 341 REMARK 465 ASP A 342 REMARK 465 ASN A 343 REMARK 465 VAL A 344 REMARK 465 GLN A 345 REMARK 465 VAL A 346 REMARK 465 ALA A 347 REMARK 465 PRO A 348 REMARK 465 GLN A 349 REMARK 465 GLU A 350 REMARK 465 VAL A 351 REMARK 465 GLU A 352 REMARK 465 VAL A 353 REMARK 465 SER A 354 REMARK 465 SER A 355 REMARK 465 TYR A 356 REMARK 465 LEU A 357 REMARK 465 VAL A 358 REMARK 465 GLY A 359 REMARK 465 GLN A 360 REMARK 465 ILE A 361 REMARK 465 ASP A 362 REMARK 465 SER A 363 REMARK 465 GLU A 364 REMARK 465 VAL A 365 REMARK 465 ASP A 366 REMARK 465 THR A 367 REMARK 465 ASP A 368 REMARK 465 ASP A 369 REMARK 465 LEU A 370 REMARK 465 SER A 371 REMARK 465 ASN A 372 REMARK 465 PHE A 373 REMARK 465 GLN A 374 REMARK 465 LEU A 375 REMARK 465 SER B 341 REMARK 465 ASP B 342 REMARK 465 ASN B 343 REMARK 465 VAL B 344 REMARK 465 GLN B 345 REMARK 465 VAL B 346 REMARK 465 ALA B 347 REMARK 465 PRO B 348 REMARK 465 GLN B 349 REMARK 465 GLU B 350 REMARK 465 VAL B 351 REMARK 465 GLU B 352 REMARK 465 VAL B 353 REMARK 465 SER B 354 REMARK 465 SER B 355 REMARK 465 TYR B 356 REMARK 465 LEU B 357 REMARK 465 VAL B 358 REMARK 465 GLY B 359 REMARK 465 GLN B 360 REMARK 465 ILE B 361 REMARK 465 ASP B 362 REMARK 465 SER B 363 REMARK 465 GLU B 364 REMARK 465 VAL B 365 REMARK 465 ASP B 366 REMARK 465 THR B 367 REMARK 465 ASP B 368 REMARK 465 ASP B 369 REMARK 465 LEU B 370 REMARK 465 SER B 371 REMARK 465 ASN B 372 REMARK 465 PHE B 373 REMARK 465 GLN B 374 REMARK 465 LEU B 375 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 GLN A 7 CG CD OE1 NE2 REMARK 470 GLN B 7 CG CD OE1 NE2 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 CYS B 196 CB CYS B 196 SG 0.206 REMARK 500 CYS B 214 CB CYS B 214 SG 0.120 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 CYS B 214 CA - CB - SG ANGL. DEV. = 8.2 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 PHE A 5 89.38 -157.73 REMARK 500 ASN A 24 -79.40 -97.18 REMARK 500 THR A 142 -152.72 -83.93 REMARK 500 ASN A 143 92.80 69.42 REMARK 500 ASP A 257 -136.53 -105.95 REMARK 500 SER A 295 -168.77 -112.39 REMARK 500 PHE B 5 94.11 -160.51 REMARK 500 ASN B 24 -81.47 -96.60 REMARK 500 ASP B 132 86.71 74.94 REMARK 500 GLN B 147 48.60 -71.68 REMARK 500 PHE B 291 42.14 -109.08 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 FE A 376 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 84 OE1 REMARK 620 2 GLU A 84 OE2 59.1 REMARK 620 3 GLU A 115 OE1 148.0 88.9 REMARK 620 4 HIS A 118 ND1 99.8 111.5 90.7 REMARK 620 5 GLU A 238 OE2 108.5 146.6 98.9 100.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 377 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 115 OE2 REMARK 620 2 GLU A 204 OE1 123.8 REMARK 620 3 GLU A 238 OE1 138.3 79.1 REMARK 620 4 HIS A 241 ND1 102.9 111.2 98.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 378 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 194 OH REMARK 620 2 ALA A 265 O 83.7 REMARK 620 3 CYS A 272 SG 93.8 110.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 379 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 196 O REMARK 620 2 CYS A 196 SG 75.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 380 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 210 O REMARK 620 2 CYS A 214 SG 94.1 REMARK 620 3 CYS A 214 N 69.2 71.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 382 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 264 O REMARK 620 2 CYS A 268 N 47.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 381 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 284 NZ REMARK 620 2 GLU A 309 OE2 55.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 376 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 84 OE1 REMARK 620 2 GLU B 84 OE2 60.3 REMARK 620 3 GLU B 115 OE1 88.9 149.2 REMARK 620 4 HIS B 118 ND1 109.8 99.4 89.1 REMARK 620 5 GLU B 238 OE2 152.8 108.3 100.1 96.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 377 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 115 OE2 REMARK 620 2 GLU B 204 OE1 125.1 REMARK 620 3 GLU B 238 OE1 137.8 81.4 REMARK 620 4 HIS B 241 ND1 99.7 108.6 101.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 378 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 196 SG REMARK 620 2 CYS B 196 O 67.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 381 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 198 SD REMARK 620 2 CYS B 272 SG 83.6 REMARK 620 3 CYS B 272 O 125.6 101.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 380 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL B 210 O REMARK 620 2 CYS B 214 SG 79.0 REMARK 620 3 CYS B 214 N 67.5 76.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 379 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 268 SG REMARK 620 2 CYS B 268 O 84.2 REMARK 620 3 CYS B 272 SG 171.4 103.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 376 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 377 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 376 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 377 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 379 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 379 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 382 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PIM RELATED DB: PDB REMARK 900 DITHIONITE REDUCED E. COLI RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT, REMARK 900 D84E MUTANT REMARK 900 RELATED ID: 1PIU RELATED DB: PDB REMARK 900 OXIDIZED RIBONUCLEOTIDE REDUCTASE R2-D84E MUTANT CONTAINING OXO- REMARK 900 BRIDGED DIFERRIC CLUSTER REMARK 900 RELATED ID: 1PIY RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R2 SOAKED WITH FERROUS ION AT NEUTRAL PH REMARK 900 RELATED ID: 1PIZ RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R2 D84E MUTANT SOAKED WITH FERROUS IONS AT REMARK 900 NEUTRAL PH REMARK 900 RELATED ID: 1PJ1 RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F SOAKED WITH FERROUS IONS AT REMARK 900 PH 5 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONFLICTS ARE DUE TO A MODELLING ERROR REMARK 999 IN THE INITIAL MODEL. DBREF 1PJ0 A 1 375 UNP P69924 RIR2_ECOLI 1 375 DBREF 1PJ0 B 1 375 UNP P69924 RIR2_ECOLI 1 375 SEQADV 1PJ0 PHE A 48 UNP P69924 TRP 48 ENGINEERED MUTATION SEQADV 1PJ0 GLU A 84 UNP P69924 ASP 84 ENGINEERED MUTATION SEQADV 1PJ0 ASN A 326 UNP P69924 GLN 326 SEE REMARK 999 SEQADV 1PJ0 PHE B 48 UNP P69924 TRP 48 ENGINEERED MUTATION SEQADV 1PJ0 GLU B 84 UNP P69924 ASP 84 ENGINEERED MUTATION SEQADV 1PJ0 ASN B 326 UNP P69924 GLN 326 SEE REMARK 999 SEQRES 1 A 375 ALA TYR THR THR PHE SER GLN THR LYS ASN ASP GLN LEU SEQRES 2 A 375 LYS GLU PRO MET PHE PHE GLY GLN PRO VAL ASN VAL ALA SEQRES 3 A 375 ARG TYR ASP GLN GLN LYS TYR ASP ILE PHE GLU LYS LEU SEQRES 4 A 375 ILE GLU LYS GLN LEU SER PHE PHE PHE ARG PRO GLU GLU SEQRES 5 A 375 VAL ASP VAL SER ARG ASP ARG ILE ASP TYR GLN ALA LEU SEQRES 6 A 375 PRO GLU HIS GLU LYS HIS ILE PHE ILE SER ASN LEU LYS SEQRES 7 A 375 TYR GLN THR LEU LEU GLU SER ILE GLN GLY ARG SER PRO SEQRES 8 A 375 ASN VAL ALA LEU LEU PRO LEU ILE SER ILE PRO GLU LEU SEQRES 9 A 375 GLU THR TRP VAL GLU THR TRP ALA PHE SER GLU THR ILE SEQRES 10 A 375 HIS SER ARG SER TYR THR HIS ILE ILE ARG ASN ILE VAL SEQRES 11 A 375 ASN ASP PRO SER VAL VAL PHE ASP ASP ILE VAL THR ASN SEQRES 12 A 375 GLU GLN ILE GLN LYS ARG ALA GLU GLY ILE SER SER TYR SEQRES 13 A 375 TYR ASP GLU LEU ILE GLU MET THR SER TYR TRP HIS LEU SEQRES 14 A 375 LEU GLY GLU GLY THR HIS THR VAL ASN GLY LYS THR VAL SEQRES 15 A 375 THR VAL SER LEU ARG GLU LEU LYS LYS LYS LEU TYR LEU SEQRES 16 A 375 CYS LEU MET SER VAL ASN ALA LEU GLU ALA ILE ARG PHE SEQRES 17 A 375 TYR VAL SER PHE ALA CYS SER PHE ALA PHE ALA GLU ARG SEQRES 18 A 375 GLU LEU MET GLU GLY ASN ALA LYS ILE ILE ARG LEU ILE SEQRES 19 A 375 ALA ARG ASP GLU ALA LEU HIS LEU THR GLY THR GLN HIS SEQRES 20 A 375 MET LEU ASN LEU LEU ARG SER GLY ALA ASP ASP PRO GLU SEQRES 21 A 375 MET ALA GLU ILE ALA GLU GLU CYS LYS GLN GLU CYS TYR SEQRES 22 A 375 ASP LEU PHE VAL GLN ALA ALA GLN GLN GLU LYS ASP TRP SEQRES 23 A 375 ALA ASP TYR LEU PHE ARG ASP GLY SER MET ILE GLY LEU SEQRES 24 A 375 ASN LYS ASP ILE LEU CYS GLN TYR VAL GLU TYR ILE THR SEQRES 25 A 375 ASN ILE ARG MET GLN ALA VAL GLY LEU ASP LEU PRO PHE SEQRES 26 A 375 ASN THR ARG SER ASN PRO ILE PRO TRP ILE ASN THR TRP SEQRES 27 A 375 LEU VAL SER ASP ASN VAL GLN VAL ALA PRO GLN GLU VAL SEQRES 28 A 375 GLU VAL SER SER TYR LEU VAL GLY GLN ILE ASP SER GLU SEQRES 29 A 375 VAL ASP THR ASP ASP LEU SER ASN PHE GLN LEU SEQRES 1 B 375 ALA TYR THR THR PHE SER GLN THR LYS ASN ASP GLN LEU SEQRES 2 B 375 LYS GLU PRO MET PHE PHE GLY GLN PRO VAL ASN VAL ALA SEQRES 3 B 375 ARG TYR ASP GLN GLN LYS TYR ASP ILE PHE GLU LYS LEU SEQRES 4 B 375 ILE GLU LYS GLN LEU SER PHE PHE PHE ARG PRO GLU GLU SEQRES 5 B 375 VAL ASP VAL SER ARG ASP ARG ILE ASP TYR GLN ALA LEU SEQRES 6 B 375 PRO GLU HIS GLU LYS HIS ILE PHE ILE SER ASN LEU LYS SEQRES 7 B 375 TYR GLN THR LEU LEU GLU SER ILE GLN GLY ARG SER PRO SEQRES 8 B 375 ASN VAL ALA LEU LEU PRO LEU ILE SER ILE PRO GLU LEU SEQRES 9 B 375 GLU THR TRP VAL GLU THR TRP ALA PHE SER GLU THR ILE SEQRES 10 B 375 HIS SER ARG SER TYR THR HIS ILE ILE ARG ASN ILE VAL SEQRES 11 B 375 ASN ASP PRO SER VAL VAL PHE ASP ASP ILE VAL THR ASN SEQRES 12 B 375 GLU GLN ILE GLN LYS ARG ALA GLU GLY ILE SER SER TYR SEQRES 13 B 375 TYR ASP GLU LEU ILE GLU MET THR SER TYR TRP HIS LEU SEQRES 14 B 375 LEU GLY GLU GLY THR HIS THR VAL ASN GLY LYS THR VAL SEQRES 15 B 375 THR VAL SER LEU ARG GLU LEU LYS LYS LYS LEU TYR LEU SEQRES 16 B 375 CYS LEU MET SER VAL ASN ALA LEU GLU ALA ILE ARG PHE SEQRES 17 B 375 TYR VAL SER PHE ALA CYS SER PHE ALA PHE ALA GLU ARG SEQRES 18 B 375 GLU LEU MET GLU GLY ASN ALA LYS ILE ILE ARG LEU ILE SEQRES 19 B 375 ALA ARG ASP GLU ALA LEU HIS LEU THR GLY THR GLN HIS SEQRES 20 B 375 MET LEU ASN LEU LEU ARG SER GLY ALA ASP ASP PRO GLU SEQRES 21 B 375 MET ALA GLU ILE ALA GLU GLU CYS LYS GLN GLU CYS TYR SEQRES 22 B 375 ASP LEU PHE VAL GLN ALA ALA GLN GLN GLU LYS ASP TRP SEQRES 23 B 375 ALA ASP TYR LEU PHE ARG ASP GLY SER MET ILE GLY LEU SEQRES 24 B 375 ASN LYS ASP ILE LEU CYS GLN TYR VAL GLU TYR ILE THR SEQRES 25 B 375 ASN ILE ARG MET GLN ALA VAL GLY LEU ASP LEU PRO PHE SEQRES 26 B 375 ASN THR ARG SER ASN PRO ILE PRO TRP ILE ASN THR TRP SEQRES 27 B 375 LEU VAL SER ASP ASN VAL GLN VAL ALA PRO GLN GLU VAL SEQRES 28 B 375 GLU VAL SER SER TYR LEU VAL GLY GLN ILE ASP SER GLU SEQRES 29 B 375 VAL ASP THR ASP ASP LEU SER ASN PHE GLN LEU HET FE A 376 1 HET FE A 377 1 HET HG A 378 1 HET HG A 379 1 HET HG A 380 1 HET HG A 381 1 HET HG A 382 1 HET FE B 376 1 HET FE B 377 1 HET HG B 378 1 HET HG B 379 1 HET HG B 380 1 HET HG B 381 1 HETNAM FE FE (III) ION HETNAM HG MERCURY (II) ION FORMUL 3 FE 4(FE 3+) FORMUL 5 HG 9(HG 2+) FORMUL 16 HOH *254(H2 O) HELIX 1 1 TYR A 33 PHE A 46 1 14 HELIX 2 2 ARG A 49 VAL A 53 5 5 HELIX 3 3 VAL A 55 LEU A 65 1 11 HELIX 4 4 PRO A 66 LEU A 96 1 31 HELIX 5 5 PRO A 97 ILE A 99 5 3 HELIX 6 6 ILE A 101 VAL A 130 1 30 HELIX 7 7 ASP A 132 THR A 142 1 11 HELIX 8 8 ASN A 143 GLU A 151 1 9 HELIX 9 9 GLY A 152 GLY A 171 1 20 HELIX 10 10 SER A 185 ILE A 206 1 22 HELIX 11 11 ILE A 206 GLU A 220 1 15 HELIX 12 12 MET A 224 SER A 254 1 31 HELIX 13 13 ASP A 258 PHE A 291 1 34 HELIX 14 14 ASN A 300 VAL A 319 1 20 HELIX 15 15 ILE A 332 ASN A 336 5 5 HELIX 16 16 TYR B 33 PHE B 46 1 14 HELIX 17 17 ARG B 49 VAL B 53 5 5 HELIX 18 18 ARG B 57 LEU B 65 1 9 HELIX 19 19 PRO B 66 LEU B 96 1 31 HELIX 20 20 PRO B 97 ILE B 99 5 3 HELIX 21 21 ILE B 101 VAL B 130 1 30 HELIX 22 22 ASP B 132 ASN B 143 1 12 HELIX 23 23 LYS B 148 GLY B 171 1 24 HELIX 24 24 SER B 185 ILE B 206 1 22 HELIX 25 25 ILE B 206 ARG B 221 1 16 HELIX 26 26 MET B 224 GLY B 255 1 32 HELIX 27 27 ASP B 258 CYS B 268 1 11 HELIX 28 28 CYS B 268 PHE B 291 1 24 HELIX 29 29 ASN B 300 VAL B 319 1 20 HELIX 30 30 ILE B 332 TRP B 338 5 7 SHEET 1 A 2 GLY A 173 VAL A 177 0 SHEET 2 A 2 LYS A 180 VAL A 184 -1 O VAL A 182 N HIS A 175 SHEET 1 B 2 GLY B 173 VAL B 177 0 SHEET 2 B 2 LYS B 180 VAL B 184 -1 O VAL B 182 N HIS B 175 SSBOND 1 CYS A 268 CYS A 272 1555 1555 2.70 LINK OE1 GLU A 84 FE FE A 376 1555 1555 2.16 LINK OE2 GLU A 84 FE FE A 376 1555 1555 2.26 LINK OE1 GLU A 115 FE FE A 376 1555 1555 2.13 LINK OE2 GLU A 115 FE FE A 377 1555 1555 1.95 LINK ND1 HIS A 118 FE FE A 376 1555 1555 2.11 LINK OH TYR A 194 HG HG A 378 1555 1555 2.79 LINK O CYS A 196 HG HG A 379 1555 1555 3.13 LINK SG CYS A 196 HG HG A 379 1555 1555 2.29 LINK OE1 GLU A 204 FE FE A 377 1555 1555 2.01 LINK O VAL A 210 HG HG A 380 1555 1555 2.83 LINK SG CYS A 214 HG HG A 380 1555 1555 2.28 LINK N CYS A 214 HG HG A 380 1555 1555 3.25 LINK OE2 GLU A 238 FE FE A 376 1555 1555 1.96 LINK OE1 GLU A 238 FE FE A 377 1555 1555 1.93 LINK ND1 HIS A 241 FE FE A 377 1555 1555 2.11 LINK O ILE A 264 HG HG A 382 1555 1555 3.48 LINK O ALA A 265 HG HG A 378 1555 1555 3.48 LINK N CYS A 268 HG HG A 382 1555 1555 3.11 LINK SG CYS A 272 HG HG A 378 1555 1555 2.39 LINK NZ LYS A 284 HG HG A 381 1555 1555 3.42 LINK OE2 GLU A 309 HG HG A 381 1555 1555 3.09 LINK OE1 GLU B 84 FE FE B 376 1555 1555 2.27 LINK OE2 GLU B 84 FE FE B 376 1555 1555 2.10 LINK OE1 GLU B 115 FE FE B 376 1555 1555 2.13 LINK OE2 GLU B 115 FE FE B 377 1555 1555 2.05 LINK ND1 HIS B 118 FE FE B 376 1555 1555 2.03 LINK SG CYS B 196 HG HG B 378 1555 1555 2.92 LINK O CYS B 196 HG HG B 378 1555 1555 3.10 LINK SD MET B 198 HG HG B 381 1555 1555 3.53 LINK OE1 GLU B 204 FE FE B 377 1555 1555 1.98 LINK O VAL B 210 HG HG B 380 1555 1555 2.77 LINK SG CYS B 214 HG HG B 380 1555 1555 2.64 LINK N CYS B 214 HG HG B 380 1555 1555 3.10 LINK OE2 GLU B 238 FE FE B 376 1555 1555 2.03 LINK OE1 GLU B 238 FE FE B 377 1555 1555 1.87 LINK ND1 HIS B 241 FE FE B 377 1555 1555 2.11 LINK SG CYS B 268 HG HG B 379 1555 1555 2.47 LINK O CYS B 268 HG HG B 379 1555 1555 2.58 LINK SG CYS B 272 HG HG B 379 1555 1555 2.30 LINK SG CYS B 272 HG HG B 381 1555 1555 3.27 LINK O CYS B 272 HG HG B 381 1555 1555 2.75 SITE 1 AC1 4 GLU A 84 GLU A 115 HIS A 118 GLU A 238 SITE 1 AC2 5 TRP A 111 GLU A 115 GLU A 204 GLU A 238 SITE 2 AC2 5 HIS A 241 SITE 1 AC3 4 GLU B 84 GLU B 115 HIS B 118 GLU B 238 SITE 1 AC4 5 TRP B 111 GLU B 115 GLU B 204 GLU B 238 SITE 2 AC4 5 HIS B 241 SITE 1 AC5 3 TYR A 194 ALA A 265 CYS A 272 SITE 1 AC6 2 TYR A 157 CYS A 196 SITE 1 AC7 2 VAL A 210 CYS A 214 SITE 1 AC8 4 TYR B 156 TYR B 157 CYS B 196 VAL B 200 SITE 1 AC9 3 TYR B 194 CYS B 268 CYS B 272 SITE 1 BC1 4 VAL B 210 ALA B 213 CYS B 214 LEU B 304 SITE 1 BC2 4 LYS A 284 CYS A 305 GLN A 306 GLU A 309 SITE 1 BC3 3 MET B 198 CYS B 272 LEU B 275 SITE 1 BC4 2 ILE A 264 CYS A 268 CRYST1 74.000 84.400 114.600 90.00 90.00 90.00 P 21 21 21 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 0.013514 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008726 0.00000