HEADER OXIDOREDUCTASE 12-FEB-19 6QOB TITLE CRYSTAL STRUCTURE OF RIBONUCLEOTIDE REDUCTASE NRDF FROM BACILLUS TITLE 2 ANTHRACIS WITH PARTIALLY OXIDISED DI-IRON METALLOCOFACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.17.4.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS ANTHRACIS; SOURCE 3 ORGANISM_TAXID: 1392; SOURCE 4 VARIANT: PXO1-/PXO2- DEFICIENT; SOURCE 5 GENE: NRDF, GBAA_1372; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 KEYWDS METAL BINDING; OXIDATION REDUCTION PROCESS; 2'-DEOXYRIBONUCLEOTIDE KEYWDS 2 METABOLISM; DNA REPLICATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.GRAVE,M.HOGBOM REVDAT 4 24-JAN-24 6QOB 1 LINK REVDAT 3 02-OCT-19 6QOB 1 JRNL REVDAT 2 28-AUG-19 6QOB 1 JRNL REVDAT 1 21-AUG-19 6QOB 0 JRNL AUTH K.GRAVE,W.LAMBERT,G.BERGGREN,J.J.GRIESE,M.D.BENNETT, JRNL AUTH 2 D.T.LOGAN,M.HOGBOM JRNL TITL REDOX-INDUCED STRUCTURAL CHANGES IN THE DI-IRON AND JRNL TITL 2 DI-MANGANESE FORMS OF BACILLUS ANTHRACIS RIBONUCLEOTIDE JRNL TITL 3 REDUCTASE SUBUNIT NRDF SUGGEST A MECHANISM FOR GATING OF JRNL TITL 4 RADICAL ACCESS. JRNL REF J.BIOL.INORG.CHEM. V. 24 849 2019 JRNL REFN ESSN 1432-1327 JRNL PMID 31410573 JRNL DOI 10.1007/S00775-019-01703-Z REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 107820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5391 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.9576 - 4.5253 0.98 3540 187 0.1747 0.2044 REMARK 3 2 4.5253 - 3.5923 1.00 3483 183 0.1425 0.1532 REMARK 3 3 3.5923 - 3.1383 1.00 3491 184 0.1574 0.1731 REMARK 3 4 3.1383 - 2.8515 1.00 3450 182 0.1655 0.1748 REMARK 3 5 2.8515 - 2.6471 1.00 3492 184 0.1553 0.1835 REMARK 3 6 2.6471 - 2.4910 1.00 3450 181 0.1428 0.1617 REMARK 3 7 2.4910 - 2.3663 1.00 3473 183 0.1441 0.1486 REMARK 3 8 2.3663 - 2.2633 1.00 3449 182 0.1470 0.1828 REMARK 3 9 2.2633 - 2.1762 1.00 3479 183 0.1494 0.1774 REMARK 3 10 2.1762 - 2.1011 1.00 3451 182 0.1574 0.1884 REMARK 3 11 2.1011 - 2.0354 1.00 3417 179 0.1621 0.1978 REMARK 3 12 2.0354 - 1.9772 1.00 3446 182 0.1637 0.1924 REMARK 3 13 1.9772 - 1.9251 0.99 3448 181 0.1675 0.1993 REMARK 3 14 1.9251 - 1.8782 1.00 3458 182 0.1693 0.2030 REMARK 3 15 1.8782 - 1.8355 1.00 3436 181 0.1728 0.2281 REMARK 3 16 1.8355 - 1.7964 1.00 3446 182 0.1764 0.2220 REMARK 3 17 1.7964 - 1.7605 1.00 3456 181 0.1884 0.2190 REMARK 3 18 1.7605 - 1.7272 1.00 3391 179 0.1865 0.2243 REMARK 3 19 1.7272 - 1.6964 1.00 3493 184 0.1930 0.2156 REMARK 3 20 1.6964 - 1.6676 1.00 3409 179 0.2001 0.2253 REMARK 3 21 1.6676 - 1.6407 1.00 3441 181 0.2019 0.2360 REMARK 3 22 1.6407 - 1.6155 1.00 3464 182 0.2084 0.2642 REMARK 3 23 1.6155 - 1.5917 1.00 3397 178 0.2165 0.2564 REMARK 3 24 1.5917 - 1.5693 1.00 3472 183 0.2257 0.2473 REMARK 3 25 1.5693 - 1.5481 1.00 3427 181 0.2373 0.2525 REMARK 3 26 1.5481 - 1.5280 1.00 3479 183 0.2555 0.2921 REMARK 3 27 1.5280 - 1.5089 1.00 3346 176 0.2512 0.2899 REMARK 3 28 1.5089 - 1.4907 1.00 3517 185 0.2691 0.2727 REMARK 3 29 1.4907 - 1.4734 1.00 3392 179 0.2839 0.3060 REMARK 3 30 1.4734 - 1.4568 0.68 2336 122 0.2998 0.2608 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 4952 REMARK 3 ANGLE : 1.180 6722 REMARK 3 CHIRALITY : 0.082 736 REMARK 3 PLANARITY : 0.008 859 REMARK 3 DIHEDRAL : 20.869 1842 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6QOB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107862 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.457 REMARK 200 RESOLUTION RANGE LOW (A) : 45.935 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6QO5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 - 2.0 M AMMONIUM SULPHATE, 0.1 M REMARK 280 BIS-TRIS METHANE PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.18850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 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 THR A 289 REMARK 465 ASP A 290 REMARK 465 THR A 291 REMARK 465 LYS 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 VAL A 299 REMARK 465 LYS A 300 REMARK 465 GLY A 301 REMARK 465 ASN A 302 REMARK 465 GLY A 303 REMARK 465 TYR A 304 REMARK 465 VAL A 305 REMARK 465 LYS A 306 REMARK 465 ALA A 307 REMARK 465 THR A 308 REMARK 465 ASN A 309 REMARK 465 VAL A 310 REMARK 465 GLU A 311 REMARK 465 LYS A 312 REMARK 465 LEU A 313 REMARK 465 SER A 314 REMARK 465 ASP A 315 REMARK 465 ASP A 316 REMARK 465 ASP A 317 REMARK 465 PHE A 318 REMARK 465 VAL A 319 REMARK 465 PHE A 320 REMARK 465 ASN A 321 REMARK 465 PHE A 322 REMARK 465 ARG B 288 REMARK 465 THR B 289 REMARK 465 ASP B 290 REMARK 465 THR B 291 REMARK 465 LYS B 292 REMARK 465 ASN B 293 REMARK 465 HIS B 294 REMARK 465 ASP B 295 REMARK 465 PHE B 296 REMARK 465 PHE B 297 REMARK 465 SER B 298 REMARK 465 VAL B 299 REMARK 465 LYS B 300 REMARK 465 GLY B 301 REMARK 465 ASN B 302 REMARK 465 GLY B 303 REMARK 465 TYR B 304 REMARK 465 VAL B 305 REMARK 465 LYS B 306 REMARK 465 ALA B 307 REMARK 465 THR B 308 REMARK 465 ASN B 309 REMARK 465 VAL B 310 REMARK 465 GLU B 311 REMARK 465 LYS B 312 REMARK 465 LEU B 313 REMARK 465 SER B 314 REMARK 465 ASP B 315 REMARK 465 ASP B 316 REMARK 465 ASP B 317 REMARK 465 PHE B 318 REMARK 465 VAL B 319 REMARK 465 PHE B 320 REMARK 465 ASN B 321 REMARK 465 PHE B 322 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 HE2 PHE B 165 OE1 GLU B 195 1.46 REMARK 500 OE2 GLU A 161 OE2 GLU A 195 1.73 REMARK 500 CE2 PHE B 165 OE1 GLU B 195 1.79 REMARK 500 OE1 GLU B 161 OE2 GLU B 195 1.87 REMARK 500 OE2 GLU B 195 O HOH B 501 2.06 REMARK 500 OE2 GLU A 195 O HOH A 501 2.08 REMARK 500 OE1 GLN B 222 O HOH B 502 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 30 CD GLU A 30 OE2 -0.077 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 GLU A 68 -48.91 -138.37 REMARK 500 TYR A 163 -60.42 -133.23 REMARK 500 GLU B 68 -49.14 -139.65 REMARK 500 TYR B 163 -62.48 -135.58 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 403 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 62 OD1 REMARK 620 2 ASP A 62 OD1 29.8 REMARK 620 3 ASP A 62 OD2 23.5 51.7 REMARK 620 4 GLU A 93 OE2 80.5 73.9 97.0 REMARK 620 5 HIS A 96 ND1 113.4 142.1 95.0 96.3 REMARK 620 6 HOH A 501 O 146.2 116.6 166.6 84.2 98.1 REMARK 620 7 HOH A 559 O 102.1 97.8 92.5 158.7 101.8 82.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 93 OE1 REMARK 620 2 GLU A 161 OE1 75.0 REMARK 620 3 GLU A 161 OE2 127.3 52.7 REMARK 620 4 GLU A 161 OE2 87.3 16.4 43.0 REMARK 620 5 GLU A 195 OE2 170.3 101.5 48.9 91.1 REMARK 620 6 HIS A 198 ND1 87.7 99.0 104.0 88.9 101.8 REMARK 620 7 HOH A 501 O 118.3 164.3 112.9 154.4 64.1 90.3 REMARK 620 8 HOH A 511 O 92.6 82.9 77.3 93.0 78.0 178.1 87.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 405 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 62 OD1 REMARK 620 2 ASP B 62 OD1 32.7 REMARK 620 3 ASP B 62 OD2 25.3 52.8 REMARK 620 4 GLU B 93 OE2 83.2 73.0 106.7 REMARK 620 5 HIS B 96 ND1 110.1 141.4 96.8 99.0 REMARK 620 6 HOH B 501 O 151.2 118.6 160.0 84.8 97.5 REMARK 620 7 HOH B 541 O 104.5 99.2 87.2 152.7 102.7 76.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 406 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 93 OE1 REMARK 620 2 GLU B 161 OE1 82.4 REMARK 620 3 GLU B 161 OE1 121.6 40.8 REMARK 620 4 GLU B 195 OE2 172.8 94.3 54.1 REMARK 620 5 HIS B 198 ND1 86.3 92.1 104.4 100.2 REMARK 620 6 HOH B 501 O 121.5 156.1 116.1 62.1 88.8 REMARK 620 7 HOH B 525 O 91.3 90.4 79.3 82.3 176.3 90.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTB A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTB B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6QO5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APO (METAL-FREE) RIBONUCLEOTIDE REDUCTASE NRDF REMARK 900 FROM BACILLUS ANTHRACIS REMARK 900 RELATED ID: 6QO9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBONUCLEOTIDE REDUCTASE NRDF FROM BACILLUS REMARK 900 ANTHRACIS SOAKED WITH MANGANESE IONS DBREF 6QOB A 1 322 UNP Q81TB4 Q81TB4_BACAN 1 322 DBREF 6QOB B 1 322 UNP Q81TB4 Q81TB4_BACAN 1 322 SEQRES 1 A 322 MET ARG ALA VAL ASN TRP ASN LYS LYS GLU ASP ASP PHE SEQRES 2 A 322 SER LEU MET PHE TRP LYS GLN ASN ILE ALA GLN PHE TRP SEQRES 3 A 322 THR GLU GLU GLU ILE ALA VAL SER SER ASP LYS ASN THR SEQRES 4 A 322 TRP VAL GLN LEU SER LYS GLU GLU GLN ILE ALA TYR LYS SEQRES 5 A 322 ARG VAL LEU GLY GLY LEU THR LEU LEU ASP THR LYS GLN SEQRES 6 A 322 GLY GLY GLU GLY MET PRO LEU VAL LEU VAL HIS LEU GLU SEQRES 7 A 322 ASN LEU GLN ALA LYS SER VAL LEU ALA PHE MET GLY ALA SEQRES 8 A 322 MET GLU GLU VAL HIS ALA LYS SER TYR SER HIS ILE PHE SEQRES 9 A 322 THR THR LEU ALA THR GLU GLU GLU ILE ASP GLU ILE PHE SEQRES 10 A 322 ASP TRP VAL ASP THR HIS PRO LEU LEU GLU LYS LYS ALA SEQRES 11 A 322 GLY ILE ILE THR SER TYR TYR ARG ARG LEU LEU LYS PRO SEQRES 12 A 322 GLU VAL THR LYS LYS GLU LEU TYR MET ALA MET VAL ALA SEQRES 13 A 322 SER VAL PHE LEU GLU SER TYR LEU PHE TYR SER GLY PHE SEQRES 14 A 322 PHE TYR PRO LEU TYR LEU ALA GLY GLN GLY LYS LEU THR SEQRES 15 A 322 ALA SER GLY GLU ILE ILE ASN LEU ILE ILE ARG ASP GLU SEQRES 16 A 322 SER ILE HIS GLY VAL PHE VAL GLY ILE LEU ALA GLN GLN SEQRES 17 A 322 ILE PHE ALA GLU LEU SER ALA GLU ASP GLN GLN GLU VAL SEQRES 18 A 322 GLN LYS GLU THR GLN GLU LEU LEU MET GLU LEU TYR GLU SEQRES 19 A 322 ILE GLU MET ALA TYR THR GLU GLU ILE TYR THR SER ILE SEQRES 20 A 322 GLY LEU VAL GLU ASP VAL ASN ARG PHE VAL ARG TYR ASN SEQRES 21 A 322 ALA ASN LYS GLY LEU MET ASN LEU GLY LEU GLU PRO LYS SEQRES 22 A 322 PHE GLU GLU GLU GLU ILE ASN PRO ILE VAL LEU ASN GLY SEQRES 23 A 322 LEU ARG THR ASP THR LYS ASN HIS ASP PHE PHE SER VAL SEQRES 24 A 322 LYS GLY ASN GLY TYR VAL LYS ALA THR ASN VAL GLU LYS SEQRES 25 A 322 LEU SER ASP ASP ASP PHE VAL PHE ASN PHE SEQRES 1 B 322 MET ARG ALA VAL ASN TRP ASN LYS LYS GLU ASP ASP PHE SEQRES 2 B 322 SER LEU MET PHE TRP LYS GLN ASN ILE ALA GLN PHE TRP SEQRES 3 B 322 THR GLU GLU GLU ILE ALA VAL SER SER ASP LYS ASN THR SEQRES 4 B 322 TRP VAL GLN LEU SER LYS GLU GLU GLN ILE ALA TYR LYS SEQRES 5 B 322 ARG VAL LEU GLY GLY LEU THR LEU LEU ASP THR LYS GLN SEQRES 6 B 322 GLY GLY GLU GLY MET PRO LEU VAL LEU VAL HIS LEU GLU SEQRES 7 B 322 ASN LEU GLN ALA LYS SER VAL LEU ALA PHE MET GLY ALA SEQRES 8 B 322 MET GLU GLU VAL HIS ALA LYS SER TYR SER HIS ILE PHE SEQRES 9 B 322 THR THR LEU ALA THR GLU GLU GLU ILE ASP GLU ILE PHE SEQRES 10 B 322 ASP TRP VAL ASP THR HIS PRO LEU LEU GLU LYS LYS ALA SEQRES 11 B 322 GLY ILE ILE THR SER TYR TYR ARG ARG LEU LEU LYS PRO SEQRES 12 B 322 GLU VAL THR LYS LYS GLU LEU TYR MET ALA MET VAL ALA SEQRES 13 B 322 SER VAL PHE LEU GLU SER TYR LEU PHE TYR SER GLY PHE SEQRES 14 B 322 PHE TYR PRO LEU TYR LEU ALA GLY GLN GLY LYS LEU THR SEQRES 15 B 322 ALA SER GLY GLU ILE ILE ASN LEU ILE ILE ARG ASP GLU SEQRES 16 B 322 SER ILE HIS GLY VAL PHE VAL GLY ILE LEU ALA GLN GLN SEQRES 17 B 322 ILE PHE ALA GLU LEU SER ALA GLU ASP GLN GLN GLU VAL SEQRES 18 B 322 GLN LYS GLU THR GLN GLU LEU LEU MET GLU LEU TYR GLU SEQRES 19 B 322 ILE GLU MET ALA TYR THR GLU GLU ILE TYR THR SER ILE SEQRES 20 B 322 GLY LEU VAL GLU ASP VAL ASN ARG PHE VAL ARG TYR ASN SEQRES 21 B 322 ALA ASN LYS GLY LEU MET ASN LEU GLY LEU GLU PRO LYS SEQRES 22 B 322 PHE GLU GLU GLU GLU ILE ASN PRO ILE VAL LEU ASN GLY SEQRES 23 B 322 LEU ARG THR ASP THR LYS ASN HIS ASP PHE PHE SER VAL SEQRES 24 B 322 LYS GLY ASN GLY TYR VAL LYS ALA THR ASN VAL GLU LYS SEQRES 25 B 322 LEU SER ASP ASP ASP PHE VAL PHE ASN PHE HET SO4 A 401 5 HET FE A 402 1 HET FE A 403 1 HET SO4 A 404 5 HET BTB A 405 33 HET BTB B 401 33 HET SO4 B 402 5 HET SO4 B 403 5 HET SO4 B 404 5 HET FE B 405 1 HET FE B 406 1 HETNAM SO4 SULFATE ION HETNAM FE FE (III) ION HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETSYN BTB BIS-TRIS BUFFER FORMUL 3 SO4 5(O4 S 2-) FORMUL 4 FE 4(FE 3+) FORMUL 7 BTB 2(C8 H19 N O5) FORMUL 14 HOH *357(H2 O) HELIX 1 AA1 PHE A 13 GLN A 24 1 12 HELIX 2 AA2 THR A 27 ILE A 31 5 5 HELIX 3 AA3 VAL A 33 SER A 35 5 3 HELIX 4 AA4 ASP A 36 VAL A 41 1 6 HELIX 5 AA5 SER A 44 GLU A 68 1 25 HELIX 6 AA6 GLU A 68 HIS A 76 1 9 HELIX 7 AA7 ASN A 79 ALA A 108 1 30 HELIX 8 AA8 THR A 109 THR A 122 1 14 HELIX 9 AA9 HIS A 123 ARG A 139 1 17 HELIX 10 AB1 THR A 146 TYR A 163 1 18 HELIX 11 AB2 PHE A 165 GLY A 177 1 13 HELIX 12 AB3 LEU A 181 LEU A 213 1 33 HELIX 13 AB4 SER A 214 THR A 245 1 32 HELIX 14 AB5 SER A 246 GLY A 248 5 3 HELIX 15 AB6 LEU A 249 LEU A 268 1 20 HELIX 16 AB7 ASN A 280 ARG A 288 1 9 HELIX 17 AB8 PHE B 13 GLN B 24 1 12 HELIX 18 AB9 THR B 27 ILE B 31 5 5 HELIX 19 AC1 VAL B 33 SER B 35 5 3 HELIX 20 AC2 ASP B 36 VAL B 41 1 6 HELIX 21 AC3 SER B 44 GLU B 68 1 25 HELIX 22 AC4 GLU B 68 LEU B 77 1 10 HELIX 23 AC5 ASN B 79 ALA B 108 1 30 HELIX 24 AC6 THR B 109 HIS B 123 1 15 HELIX 25 AC7 HIS B 123 ARG B 139 1 17 HELIX 26 AC8 THR B 146 TYR B 163 1 18 HELIX 27 AC9 PHE B 165 GLY B 177 1 13 HELIX 28 AD1 LEU B 181 LEU B 213 1 33 HELIX 29 AD2 SER B 214 THR B 245 1 32 HELIX 30 AD3 SER B 246 GLY B 248 5 3 HELIX 31 AD4 LEU B 249 LEU B 268 1 20 HELIX 32 AD5 ASN B 280 LEU B 287 1 8 LINK OD1AASP A 62 FE FE A 403 1555 1555 2.15 LINK OD1BASP A 62 FE FE A 403 1555 1555 2.76 LINK OD2BASP A 62 FE FE A 403 1555 1555 1.98 LINK OE1 GLU A 93 FE FE A 402 1555 1555 1.91 LINK OE2 GLU A 93 FE FE A 403 1555 1555 2.03 LINK ND1 HIS A 96 FE FE A 403 1555 1555 2.13 LINK OE1AGLU A 161 FE FE A 402 1555 1555 2.66 LINK OE2AGLU A 161 FE FE A 402 1555 1555 2.11 LINK OE2BGLU A 161 FE FE A 402 1555 1555 1.85 LINK OE2 GLU A 195 FE FE A 402 1555 1555 2.08 LINK ND1 HIS A 198 FE FE A 402 1555 1555 2.23 LINK FE FE A 402 O HOH A 501 1555 1555 1.83 LINK FE FE A 402 O HOH A 511 1555 1555 2.28 LINK FE FE A 403 O HOH A 501 1555 1555 2.23 LINK FE FE A 403 O HOH A 559 1555 1555 1.93 LINK OD1AASP B 62 FE FE B 405 1555 1555 2.09 LINK OD1BASP B 62 FE FE B 405 1555 1555 2.72 LINK OD2BASP B 62 FE FE B 405 1555 1555 2.13 LINK OE2 GLU B 93 FE FE B 405 1555 1555 2.06 LINK OE1 GLU B 93 FE FE B 406 1555 1555 1.86 LINK ND1 HIS B 96 FE FE B 405 1555 1555 2.16 LINK OE1AGLU B 161 FE FE B 406 1555 1555 1.89 LINK OE1BGLU B 161 FE FE B 406 1555 1555 2.05 LINK OE2 GLU B 195 FE FE B 406 1555 1555 2.07 LINK ND1 HIS B 198 FE FE B 406 1555 1555 2.26 LINK FE FE B 405 O HOH B 501 1555 1555 2.25 LINK FE FE B 405 O HOH B 541 1555 1555 1.83 LINK FE FE B 406 O HOH B 501 1555 1555 1.93 LINK FE FE B 406 O HOH B 525 1555 1555 2.19 SITE 1 AC1 5 ALA A 32 VAL A 33 SER A 34 HIS A 102 SITE 2 AC1 5 HOH A 544 SITE 1 AC2 7 GLU A 93 GLU A 161 GLU A 195 HIS A 198 SITE 2 AC2 7 FE A 403 HOH A 501 HOH A 511 SITE 1 AC3 8 ASP A 62 GLU A 93 HIS A 96 GLU A 195 SITE 2 AC3 8 FE A 402 HOH A 501 HOH A 511 HOH A 559 SITE 1 AC4 4 MET A 1 ARG A 2 BTB A 405 HOH A 575 SITE 1 AC5 12 VAL A 75 HIS A 76 LEU A 77 GLU A 78 SITE 2 AC5 12 LYS A 83 PRO A 143 SO4 A 404 HOH A 549 SITE 3 AC5 12 HOH A 573 HOH A 618 GLU B 68 ARG B 138 SITE 1 AC6 11 GLU A 68 ARG A 138 VAL B 75 HIS B 76 SITE 2 AC6 11 LEU B 77 GLU B 78 LYS B 83 PRO B 143 SITE 3 AC6 11 SO4 B 404 HOH B 511 HOH B 524 SITE 1 AC7 8 SER B 44 LYS B 45 HOH B 515 HOH B 529 SITE 2 AC7 8 HOH B 540 HOH B 550 HOH B 575 HOH B 643 SITE 1 AC8 7 ALA B 32 VAL B 33 SER B 34 HIS B 102 SITE 2 AC8 7 HOH B 522 HOH B 559 HOH B 561 SITE 1 AC9 4 MET B 1 ARG B 2 BTB B 401 HOH B 579 SITE 1 AD1 7 ASP B 62 GLU B 93 HIS B 96 FE B 406 SITE 2 AD1 7 HOH B 501 HOH B 525 HOH B 541 SITE 1 AD2 7 GLU B 93 GLU B 161 GLU B 195 HIS B 198 SITE 2 AD2 7 FE B 405 HOH B 501 HOH B 525 CRYST1 57.137 60.377 95.758 90.00 106.38 90.00 P 1 21 1 4 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 0.017502 0.000000 0.005144 0.00000 SCALE2 0.000000 0.016563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010885 0.00000