HEADER DNA BINDING PROTEIN 24-JUN-21 7R7J TITLE CRYSTAL STRUCTURE OF RADD WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE DNA REPAIR HELICASE RADD; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.6.4.12; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: RADD, YEJH, YEJI, YEJJ, B2184, JW2172; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: STL2669(DE3) KEYWDS ATPASE, SF2, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.OSORIO GARCIA,K.A.SATYSHUR,J.L.KECK,M.M.COX REVDAT 3 18-OCT-23 7R7J 1 REMARK REVDAT 2 26-OCT-22 7R7J 1 JRNL REVDAT 1 13-APR-22 7R7J 0 JRNL AUTH M.A.OSORIO GARCIA,K.A.SATYSHUR,M.M.COX,J.L.KECK JRNL TITL X-RAY CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI RADD DNA JRNL TITL 2 REPAIR PROTEIN BOUND TO ADP REVEALS A NOVEL ZINC RIBBON JRNL TITL 3 DOMAIN. JRNL REF PLOS ONE V. 17 66031 2022 JRNL REFN ESSN 1932-6203 JRNL PMID 35482735 JRNL DOI 10.1371/JOURNAL.PONE.0266031 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 3 NUMBER OF REFLECTIONS : 71229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.540 REMARK 3 FREE R VALUE TEST SET COUNT : 1812 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 35.6500 - 4.7700 0.98 6508 159 0.2099 0.2411 REMARK 3 2 4.7700 - 3.7900 0.98 6466 169 0.1910 0.2173 REMARK 3 3 3.7900 - 3.3100 0.97 6455 168 0.2225 0.2635 REMARK 3 4 3.3100 - 3.0100 0.97 6361 165 0.2495 0.2544 REMARK 3 5 3.0100 - 2.7900 0.94 6159 163 0.2500 0.2640 REMARK 3 6 2.7900 - 2.6300 0.90 5952 156 0.2623 0.3210 REMARK 3 7 2.6300 - 2.5000 0.87 5803 143 0.2823 0.3043 REMARK 3 8 2.5000 - 2.3900 0.83 5437 148 0.2859 0.3203 REMARK 3 9 2.3900 - 2.3000 0.78 5163 138 0.2977 0.3684 REMARK 3 10 2.3000 - 2.2200 0.70 4593 117 0.3059 0.3713 REMARK 3 11 2.2200 - 2.1500 0.63 4192 104 0.3279 0.3594 REMARK 3 12 2.1500 - 2.0900 0.54 3560 97 0.3311 0.3588 REMARK 3 13 2.0900 - 2.0300 0.42 2768 85 0.3618 0.4371 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.293 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.13 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 : 0.003 9101 REMARK 3 ANGLE : 0.608 12372 REMARK 3 CHIRALITY : 0.042 1374 REMARK 3 PLANARITY : 0.005 1623 REMARK 3 DIHEDRAL : 9.155 1273 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 7R7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79347 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 45.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.05400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.1_4122 REMARK 200 STARTING MODEL: 6DJE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM TRIS-HCL, 100 MM POTASSIUM REMARK 280 CHLORIDE, 0.5 MM DTT, 0.5 MM MAGNESIUM CHLORIDE, 0.5 MM ATPGS, 9% REMARK 280 (W/V) PEG 3350, 75 MM SODIUM THIOCYANATE, PH 7.7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 ASP A 283 REMARK 465 THR A 284 REMARK 465 PRO A 285 REMARK 465 GLY A 286 REMARK 465 ALA A 287 REMARK 465 ARG A 579 REMARK 465 LEU A 580 REMARK 465 ALA A 581 REMARK 465 HIS A 582 REMARK 465 GLU A 583 REMARK 465 LEU A 584 REMARK 465 ARG A 585 REMARK 465 GLY A 586 REMARK 465 MET B 1 REMARK 465 LYS B 297 REMARK 465 ALA B 298 REMARK 465 GLN B 299 REMARK 465 ARG B 300 REMARK 465 LEU B 580 REMARK 465 ALA B 581 REMARK 465 HIS B 582 REMARK 465 GLU B 583 REMARK 465 LEU B 584 REMARK 465 ARG B 585 REMARK 465 GLY B 586 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 PHE A 3 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 LEU A 83 CG CD1 CD2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 GLU A 87 CG CD OE1 OE2 REMARK 470 HIS A 89 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 MET A 204 CG SD CE REMARK 470 ARG A 213 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 226 CG OD1 OD2 REMARK 470 ILE A 241 CG1 CG2 CD1 REMARK 470 GLU A 275 CG CD OE1 OE2 REMARK 470 THR A 281 OG1 CG2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 ARG A 289 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 290 CG OD1 OD2 REMARK 470 LEU A 292 CG CD1 CD2 REMARK 470 ILE A 293 CG1 CG2 CD1 REMARK 470 VAL A 309 CG1 CG2 REMARK 470 LEU A 310 CG CD1 CD2 REMARK 470 THR A 311 OG1 CG2 REMARK 470 PHE A 314 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 362 CG OD1 OD2 REMARK 470 ASP A 419 CG OD1 OD2 REMARK 470 GLN A 436 CG CD OE1 NE2 REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 463 CG CD CE NZ REMARK 470 ARG A 467 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 468 CG CD1 CD2 REMARK 470 LYS A 469 CG CD CE NZ REMARK 470 ASP A 470 CG OD1 OD2 REMARK 470 HIS A 485 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 559 CG CD NE CZ NH1 NH2 REMARK 470 MET A 560 CG SD CE REMARK 470 LYS A 561 CG CD CE NZ REMARK 470 TYR A 564 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TRP A 565 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 565 CZ3 CH2 REMARK 470 ARG A 568 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 569 CG CD OE1 OE2 REMARK 470 ARG A 577 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 578 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 75 CG CD OE1 OE2 REMARK 470 LYS B 84 CG CD CE NZ REMARK 470 ARG B 85 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 86 CG CD CE NZ REMARK 470 GLU B 87 CG CD OE1 OE2 REMARK 470 ASP B 125 CG OD1 OD2 REMARK 470 GLU B 200 CG CD OE1 OE2 REMARK 470 ARG B 201 CG CD NE CZ NH1 NH2 REMARK 470 MET B 204 CG SD CE REMARK 470 VAL B 207 CG1 CG2 REMARK 470 ARG B 213 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 214 CG CD1 CD2 REMARK 470 HIS B 240 CG ND1 CD2 CE1 NE2 REMARK 470 MET B 246 CG SD CE REMARK 470 ARG B 252 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 253 CG CD CE NZ REMARK 470 GLU B 275 CG CD OE1 OE2 REMARK 470 LEU B 279 CG CD1 CD2 REMARK 470 THR B 281 OG1 CG2 REMARK 470 ASP B 283 CG OD1 OD2 REMARK 470 THR B 284 OG1 CG2 REMARK 470 GLU B 288 CG CD OE1 OE2 REMARK 470 ASP B 290 CG OD1 OD2 REMARK 470 PHE B 296 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE B 301 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 302 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 310 CG CD1 CD2 REMARK 470 PHE B 314 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP B 320 CG OD1 OD2 REMARK 470 LEU B 321 CG CD1 CD2 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 GLN A 163 -62.37 -94.27 REMARK 500 GLU A 275 -2.50 70.27 REMARK 500 VAL A 307 -169.89 -111.56 REMARK 500 ALA A 308 72.44 -66.29 REMARK 500 LYS A 561 -168.79 -160.48 REMARK 500 TYR A 564 -53.44 -120.56 REMARK 500 GLN B 163 -61.74 -95.65 REMARK 500 ASP B 290 4.01 -68.17 REMARK 500 ILE B 293 -63.20 -97.52 REMARK 500 THR B 311 74.85 -101.33 REMARK 500 PRO B 360 59.09 -92.58 REMARK 500 ASP B 442 150.04 -49.71 REMARK 500 ASP B 486 -159.48 -149.88 REMARK 500 PHE B 523 -56.41 -120.94 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 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 38 OG REMARK 620 2 ADP A 601 O2B 117.2 REMARK 620 3 ADP A 601 O2A 139.2 65.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 384 SG REMARK 620 2 CYS A 387 SG 104.8 REMARK 620 3 CYS A 411 SG 107.3 106.2 REMARK 620 4 CYS A 425 SG 111.6 110.0 116.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 604 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 434 SG REMARK 620 2 CYS A 437 SG 118.0 REMARK 620 3 CYS A 448 SG 103.5 101.5 REMARK 620 4 CYS A 451 SG 101.5 124.5 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 38 OG REMARK 620 2 ADP B 601 O1B 113.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 384 SG REMARK 620 2 CYS B 387 SG 103.2 REMARK 620 3 CYS B 411 SG 110.2 111.1 REMARK 620 4 CYS B 425 SG 110.7 115.6 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 604 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 434 SG REMARK 620 2 CYS B 437 SG 121.5 REMARK 620 3 CYS B 448 SG 111.3 104.5 REMARK 620 4 CYS B 451 SG 110.8 108.4 97.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6JDE RELATED DB: PDB REMARK 900 HOLO ENZYME DBREF 7R7J A 1 586 UNP P33919 RADD_ECOLI 1 586 DBREF 7R7J B 1 586 UNP P33919 RADD_ECOLI 1 586 SEQRES 1 A 586 MET ILE PHE THR LEU ARG PRO TYR GLN GLN GLU ALA VAL SEQRES 2 A 586 ASP ALA THR LEU ASN HIS PHE ARG ARG HIS LYS THR PRO SEQRES 3 A 586 ALA VAL ILE VAL LEU PRO THR GLY ALA GLY LYS SER LEU SEQRES 4 A 586 VAL ILE ALA GLU LEU ALA ARG LEU ALA ARG GLY ARG VAL SEQRES 5 A 586 LEU VAL LEU ALA HIS VAL LYS GLU LEU VAL ALA GLN ASN SEQRES 6 A 586 HIS ALA LYS TYR GLN ALA LEU GLY LEU GLU ALA ASP ILE SEQRES 7 A 586 PHE ALA ALA GLY LEU LYS ARG LYS GLU SER HIS GLY LYS SEQRES 8 A 586 VAL VAL PHE GLY SER VAL GLN SER VAL ALA ARG ASN LEU SEQRES 9 A 586 ASP ALA PHE GLN GLY GLU PHE SER LEU LEU ILE VAL ASP SEQRES 10 A 586 GLU CYS HIS ARG ILE GLY ASP ASP GLU GLU SER GLN TYR SEQRES 11 A 586 GLN GLN ILE LEU THR HIS LEU THR LYS VAL ASN PRO HIS SEQRES 12 A 586 LEU ARG LEU LEU GLY LEU THR ALA THR PRO PHE ARG LEU SEQRES 13 A 586 GLY LYS GLY TRP ILE TYR GLN PHE HIS TYR HIS GLY MET SEQRES 14 A 586 VAL ARG GLY ASP GLU LYS ALA LEU PHE ARG ASP CYS ILE SEQRES 15 A 586 TYR GLU LEU PRO LEU ARG TYR MET ILE LYS HIS GLY TYR SEQRES 16 A 586 LEU THR PRO PRO GLU ARG LEU ASP MET PRO VAL VAL GLN SEQRES 17 A 586 TYR ASP PHE SER ARG LEU GLN ALA GLN SER ASN GLY LEU SEQRES 18 A 586 PHE SER GLU ALA ASP LEU ASN ARG GLU LEU LYS LYS GLN SEQRES 19 A 586 GLN ARG ILE THR PRO HIS ILE ILE SER GLN ILE MET GLU SEQRES 20 A 586 PHE ALA ALA THR ARG LYS GLY VAL MET ILE PHE ALA ALA SEQRES 21 A 586 THR VAL GLU HIS ALA LYS GLU ILE VAL GLY LEU LEU PRO SEQRES 22 A 586 ALA GLU ASP ALA ALA LEU ILE THR GLY ASP THR PRO GLY SEQRES 23 A 586 ALA GLU ARG ASP VAL LEU ILE GLU ASN PHE LYS ALA GLN SEQRES 24 A 586 ARG PHE ARG TYR LEU VAL ASN VAL ALA VAL LEU THR THR SEQRES 25 A 586 GLY PHE ASP ALA PRO HIS VAL ASP LEU ILE ALA ILE LEU SEQRES 26 A 586 ARG PRO THR GLU SER VAL SER LEU TYR GLN GLN ILE VAL SEQRES 27 A 586 GLY ARG GLY LEU ARG LEU ALA PRO GLY LYS THR ASP CYS SEQRES 28 A 586 LEU ILE LEU ASP TYR ALA GLY ASN PRO HIS ASP LEU TYR SEQRES 29 A 586 ALA PRO GLU VAL GLY THR PRO LYS GLY LYS SER ASP ASN SEQRES 30 A 586 VAL PRO VAL GLN VAL PHE CYS PRO ALA CYS GLY PHE ALA SEQRES 31 A 586 ASN THR PHE TRP GLY LYS THR THR ALA ASP GLY THR LEU SEQRES 32 A 586 ILE GLU HIS PHE GLY ARG ARG CYS GLN GLY TRP PHE GLU SEQRES 33 A 586 ASP ASP ASP GLY HIS ARG GLU GLN CYS ASP PHE ARG PHE SEQRES 34 A 586 ARG PHE LYS ASN CYS PRO GLN CYS ASN ALA GLU ASN ASP SEQRES 35 A 586 ILE ALA ALA ARG ARG CYS ARG GLU CYS ASP THR VAL LEU SEQRES 36 A 586 VAL ASP PRO ASP ASP MET LEU LYS ALA ALA LEU ARG LEU SEQRES 37 A 586 LYS ASP ALA LEU VAL LEU ARG CYS SER GLY MET SER LEU SEQRES 38 A 586 GLN HIS GLY HIS ASP GLU LYS GLY GLU TRP LEU LYS ILE SEQRES 39 A 586 THR TYR TYR ASP GLU ASP GLY ALA ASP VAL SER GLU ARG SEQRES 40 A 586 PHE ARG LEU GLN THR PRO ALA GLN ARG THR ALA PHE GLU SEQRES 41 A 586 GLN LEU PHE ILE ARG PRO HIS THR ARG THR PRO GLY ILE SEQRES 42 A 586 PRO LEU ARG TRP ILE THR ALA ALA ASP ILE LEU ALA GLN SEQRES 43 A 586 GLN ALA LEU LEU ARG HIS PRO ASP PHE VAL VAL ALA ARG SEQRES 44 A 586 MET LYS GLY GLN TYR TRP GLN VAL ARG GLU LYS VAL PHE SEQRES 45 A 586 ASP TYR GLU GLY ARG PHE ARG LEU ALA HIS GLU LEU ARG SEQRES 46 A 586 GLY SEQRES 1 B 586 MET ILE PHE THR LEU ARG PRO TYR GLN GLN GLU ALA VAL SEQRES 2 B 586 ASP ALA THR LEU ASN HIS PHE ARG ARG HIS LYS THR PRO SEQRES 3 B 586 ALA VAL ILE VAL LEU PRO THR GLY ALA GLY LYS SER LEU SEQRES 4 B 586 VAL ILE ALA GLU LEU ALA ARG LEU ALA ARG GLY ARG VAL SEQRES 5 B 586 LEU VAL LEU ALA HIS VAL LYS GLU LEU VAL ALA GLN ASN SEQRES 6 B 586 HIS ALA LYS TYR GLN ALA LEU GLY LEU GLU ALA ASP ILE SEQRES 7 B 586 PHE ALA ALA GLY LEU LYS ARG LYS GLU SER HIS GLY LYS SEQRES 8 B 586 VAL VAL PHE GLY SER VAL GLN SER VAL ALA ARG ASN LEU SEQRES 9 B 586 ASP ALA PHE GLN GLY GLU PHE SER LEU LEU ILE VAL ASP SEQRES 10 B 586 GLU CYS HIS ARG ILE GLY ASP ASP GLU GLU SER GLN TYR SEQRES 11 B 586 GLN GLN ILE LEU THR HIS LEU THR LYS VAL ASN PRO HIS SEQRES 12 B 586 LEU ARG LEU LEU GLY LEU THR ALA THR PRO PHE ARG LEU SEQRES 13 B 586 GLY LYS GLY TRP ILE TYR GLN PHE HIS TYR HIS GLY MET SEQRES 14 B 586 VAL ARG GLY ASP GLU LYS ALA LEU PHE ARG ASP CYS ILE SEQRES 15 B 586 TYR GLU LEU PRO LEU ARG TYR MET ILE LYS HIS GLY TYR SEQRES 16 B 586 LEU THR PRO PRO GLU ARG LEU ASP MET PRO VAL VAL GLN SEQRES 17 B 586 TYR ASP PHE SER ARG LEU GLN ALA GLN SER ASN GLY LEU SEQRES 18 B 586 PHE SER GLU ALA ASP LEU ASN ARG GLU LEU LYS LYS GLN SEQRES 19 B 586 GLN ARG ILE THR PRO HIS ILE ILE SER GLN ILE MET GLU SEQRES 20 B 586 PHE ALA ALA THR ARG LYS GLY VAL MET ILE PHE ALA ALA SEQRES 21 B 586 THR VAL GLU HIS ALA LYS GLU ILE VAL GLY LEU LEU PRO SEQRES 22 B 586 ALA GLU ASP ALA ALA LEU ILE THR GLY ASP THR PRO GLY SEQRES 23 B 586 ALA GLU ARG ASP VAL LEU ILE GLU ASN PHE LYS ALA GLN SEQRES 24 B 586 ARG PHE ARG TYR LEU VAL ASN VAL ALA VAL LEU THR THR SEQRES 25 B 586 GLY PHE ASP ALA PRO HIS VAL ASP LEU ILE ALA ILE LEU SEQRES 26 B 586 ARG PRO THR GLU SER VAL SER LEU TYR GLN GLN ILE VAL SEQRES 27 B 586 GLY ARG GLY LEU ARG LEU ALA PRO GLY LYS THR ASP CYS SEQRES 28 B 586 LEU ILE LEU ASP TYR ALA GLY ASN PRO HIS ASP LEU TYR SEQRES 29 B 586 ALA PRO GLU VAL GLY THR PRO LYS GLY LYS SER ASP ASN SEQRES 30 B 586 VAL PRO VAL GLN VAL PHE CYS PRO ALA CYS GLY PHE ALA SEQRES 31 B 586 ASN THR PHE TRP GLY LYS THR THR ALA ASP GLY THR LEU SEQRES 32 B 586 ILE GLU HIS PHE GLY ARG ARG CYS GLN GLY TRP PHE GLU SEQRES 33 B 586 ASP ASP ASP GLY HIS ARG GLU GLN CYS ASP PHE ARG PHE SEQRES 34 B 586 ARG PHE LYS ASN CYS PRO GLN CYS ASN ALA GLU ASN ASP SEQRES 35 B 586 ILE ALA ALA ARG ARG CYS ARG GLU CYS ASP THR VAL LEU SEQRES 36 B 586 VAL ASP PRO ASP ASP MET LEU LYS ALA ALA LEU ARG LEU SEQRES 37 B 586 LYS ASP ALA LEU VAL LEU ARG CYS SER GLY MET SER LEU SEQRES 38 B 586 GLN HIS GLY HIS ASP GLU LYS GLY GLU TRP LEU LYS ILE SEQRES 39 B 586 THR TYR TYR ASP GLU ASP GLY ALA ASP VAL SER GLU ARG SEQRES 40 B 586 PHE ARG LEU GLN THR PRO ALA GLN ARG THR ALA PHE GLU SEQRES 41 B 586 GLN LEU PHE ILE ARG PRO HIS THR ARG THR PRO GLY ILE SEQRES 42 B 586 PRO LEU ARG TRP ILE THR ALA ALA ASP ILE LEU ALA GLN SEQRES 43 B 586 GLN ALA LEU LEU ARG HIS PRO ASP PHE VAL VAL ALA ARG SEQRES 44 B 586 MET LYS GLY GLN TYR TRP GLN VAL ARG GLU LYS VAL PHE SEQRES 45 B 586 ASP TYR GLU GLY ARG PHE ARG LEU ALA HIS GLU LEU ARG SEQRES 46 B 586 GLY HET ADP A 601 39 HET MG A 602 1 HET ZN A 603 1 HET ZN A 604 1 HET ADP B 601 38 HET MG B 602 1 HET ZN B 603 1 HET ZN B 604 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 MG 2(MG 2+) FORMUL 5 ZN 4(ZN 2+) FORMUL 11 HOH *286(H2 O) HELIX 1 AA1 ARG A 6 ARG A 21 1 16 HELIX 2 AA2 GLY A 36 ALA A 48 1 13 HELIX 3 AA3 VAL A 58 ALA A 71 1 14 HELIX 4 AA4 VAL A 97 ASN A 103 1 7 HELIX 5 AA5 LEU A 104 PHE A 107 5 4 HELIX 6 AA6 CYS A 119 ILE A 122 5 4 HELIX 7 AA7 GLU A 126 ASN A 141 1 16 HELIX 8 AA8 PRO A 186 HIS A 193 1 8 HELIX 9 AA9 SER A 223 GLN A 234 1 12 HELIX 10 AB1 ILE A 237 ALA A 250 1 14 HELIX 11 AB2 THR A 261 LEU A 272 1 12 HELIX 12 AB3 LEU A 292 ALA A 298 1 7 HELIX 13 AB4 SER A 330 ARG A 340 1 11 HELIX 14 AB5 ASP A 457 LEU A 468 1 12 HELIX 15 AB6 THR A 512 PHE A 523 1 12 HELIX 16 AB7 PHE A 523 THR A 528 1 6 HELIX 17 AB8 THR A 539 GLN A 546 1 8 HELIX 18 AB9 GLN A 547 LEU A 550 5 4 HELIX 19 AC1 ARG B 6 ARG B 21 1 16 HELIX 20 AC2 GLY B 36 ALA B 48 1 13 HELIX 21 AC3 VAL B 58 ALA B 71 1 14 HELIX 22 AC4 VAL B 97 ASN B 103 1 7 HELIX 23 AC5 LEU B 104 PHE B 107 5 4 HELIX 24 AC6 CYS B 119 ILE B 122 5 4 HELIX 25 AC7 GLU B 126 ASN B 141 1 16 HELIX 26 AC8 PRO B 186 HIS B 193 1 8 HELIX 27 AC9 SER B 223 GLN B 234 1 12 HELIX 28 AD1 ILE B 237 ALA B 250 1 14 HELIX 29 AD2 THR B 261 LEU B 272 1 12 HELIX 30 AD3 SER B 330 ARG B 340 1 11 HELIX 31 AD4 ASP B 457 ARG B 467 1 11 HELIX 32 AD5 THR B 512 PHE B 523 1 12 HELIX 33 AD6 PHE B 523 THR B 528 1 6 HELIX 34 AD7 THR B 539 GLN B 546 1 8 HELIX 35 AD8 GLN B 547 LEU B 550 5 4 SHEET 1 AA1 9 ALA A 76 PHE A 79 0 SHEET 2 AA1 9 VAL A 92 SER A 96 1 O PHE A 94 N PHE A 79 SHEET 3 AA1 9 ARG A 51 ALA A 56 1 N VAL A 54 O VAL A 93 SHEET 4 AA1 9 PHE A 111 ASP A 117 1 O ILE A 115 N LEU A 53 SHEET 5 AA1 9 ARG A 145 THR A 150 1 O LEU A 147 N LEU A 114 SHEET 6 AA1 9 ALA A 27 VAL A 30 1 N ALA A 27 O GLY A 148 SHEET 7 AA1 9 PHE A 178 GLU A 184 1 O TYR A 183 N VAL A 30 SHEET 8 AA1 9 TYR A 162 HIS A 165 1 N PHE A 164 O ARG A 179 SHEET 9 AA1 9 MET A 169 VAL A 170 -1 O MET A 169 N HIS A 165 SHEET 1 AA2 2 PHE A 154 ARG A 155 0 SHEET 2 AA2 2 GLY A 159 TRP A 160 -1 O GLY A 159 N ARG A 155 SHEET 1 AA3 6 PRO A 199 ARG A 201 0 SHEET 2 AA3 6 CYS A 351 ASP A 355 1 O ILE A 353 N GLU A 200 SHEET 3 AA3 6 VAL A 319 ILE A 324 1 N ILE A 322 O LEU A 354 SHEET 4 AA3 6 GLY A 254 PHE A 258 1 N PHE A 258 O ALA A 323 SHEET 5 AA3 6 TYR A 303 ASN A 306 1 O ASN A 306 N ILE A 257 SHEET 6 AA3 6 ALA A 277 ILE A 280 1 N ALA A 278 O VAL A 305 SHEET 1 AA4 3 VAL A 378 PHE A 383 0 SHEET 2 AA4 3 ALA A 390 THR A 397 -1 O GLY A 395 N VAL A 378 SHEET 3 AA4 3 LEU A 403 HIS A 406 -1 O ILE A 404 N LYS A 396 SHEET 1 AA5 2 TRP A 414 GLU A 416 0 SHEET 2 AA5 2 ARG A 422 GLN A 424 -1 O GLU A 423 N PHE A 415 SHEET 1 AA6 2 LYS A 432 ASN A 433 0 SHEET 2 AA6 2 GLU A 440 ASN A 441 -1 O ASN A 441 N LYS A 432 SHEET 1 AA7 3 ALA A 471 ARG A 475 0 SHEET 2 AA7 3 PHE A 555 ARG A 559 -1 O ALA A 558 N LEU A 472 SHEET 3 AA7 3 GLN A 566 VAL A 571 -1 O GLU A 569 N VAL A 557 SHEET 1 AA8 3 GLY A 478 ASP A 486 0 SHEET 2 AA8 3 GLY A 489 TYR A 497 -1 O LYS A 493 N GLN A 482 SHEET 3 AA8 3 ASP A 503 ARG A 509 -1 O VAL A 504 N TYR A 496 SHEET 1 AA9 9 ALA B 76 PHE B 79 0 SHEET 2 AA9 9 VAL B 92 SER B 96 1 O PHE B 94 N PHE B 79 SHEET 3 AA9 9 ARG B 51 ALA B 56 1 N VAL B 54 O VAL B 93 SHEET 4 AA9 9 PHE B 111 ASP B 117 1 O ILE B 115 N LEU B 55 SHEET 5 AA9 9 ARG B 145 THR B 150 1 O LEU B 147 N LEU B 114 SHEET 6 AA9 9 ALA B 27 VAL B 30 1 N ALA B 27 O GLY B 148 SHEET 7 AA9 9 PHE B 178 GLU B 184 1 O ASP B 180 N VAL B 28 SHEET 8 AA9 9 TYR B 162 HIS B 165 1 N PHE B 164 O ARG B 179 SHEET 9 AA9 9 MET B 169 VAL B 170 -1 O MET B 169 N HIS B 165 SHEET 1 AB1 2 PHE B 154 ARG B 155 0 SHEET 2 AB1 2 GLY B 159 TRP B 160 -1 N GLY B 159 O ARG B 155 SHEET 1 AB2 6 PRO B 199 ARG B 201 0 SHEET 2 AB2 6 CYS B 351 ASP B 355 1 O ILE B 353 N GLU B 200 SHEET 3 AB2 6 LEU B 321 LEU B 325 1 N ILE B 322 O LEU B 352 SHEET 4 AB2 6 VAL B 255 ALA B 259 1 N PHE B 258 O ALA B 323 SHEET 5 AB2 6 TYR B 303 ASN B 306 1 O ASN B 306 N ALA B 259 SHEET 6 AB2 6 LEU B 279 ILE B 280 1 N ILE B 280 O VAL B 305 SHEET 1 AB3 3 VAL B 378 PHE B 383 0 SHEET 2 AB3 3 ALA B 390 THR B 397 -1 O PHE B 393 N VAL B 380 SHEET 3 AB3 3 LEU B 403 HIS B 406 -1 O ILE B 404 N LYS B 396 SHEET 1 AB4 2 TRP B 414 GLU B 416 0 SHEET 2 AB4 2 ARG B 422 GLN B 424 -1 O GLU B 423 N PHE B 415 SHEET 1 AB5 2 LYS B 432 ASN B 433 0 SHEET 2 AB5 2 GLU B 440 ASN B 441 -1 O ASN B 441 N LYS B 432 SHEET 1 AB6 5 ASP B 503 ARG B 509 0 SHEET 2 AB6 5 GLY B 489 ASP B 498 -1 N TYR B 496 O VAL B 504 SHEET 3 AB6 5 ALA B 471 ASP B 486 -1 N GLN B 482 O LYS B 493 SHEET 4 AB6 5 PHE B 555 LYS B 561 -1 O ALA B 558 N LEU B 472 SHEET 5 AB6 5 TYR B 564 VAL B 571 -1 O VAL B 571 N PHE B 555 LINK OG SER A 38 MG MG A 602 1555 1555 2.82 LINK SG CYS A 384 ZN ZN A 603 1555 1555 2.46 LINK SG CYS A 387 ZN ZN A 603 1555 1555 2.39 LINK SG CYS A 411 ZN ZN A 603 1555 1555 2.37 LINK SG CYS A 425 ZN ZN A 603 1555 1555 2.31 LINK SG CYS A 434 ZN ZN A 604 1555 1555 2.26 LINK SG CYS A 437 ZN ZN A 604 1555 1555 2.29 LINK SG CYS A 448 ZN ZN A 604 1555 1555 2.36 LINK SG CYS A 451 ZN ZN A 604 1555 1555 2.36 LINK O2B ADP A 601 MG MG A 602 1555 1555 2.85 LINK O2A ADP A 601 MG MG A 602 1555 1555 2.97 LINK OG SER B 38 MG MG B 602 1555 1555 2.93 LINK SG CYS B 384 ZN ZN B 603 1555 1555 2.47 LINK SG CYS B 387 ZN ZN B 603 1555 1555 2.40 LINK SG CYS B 411 ZN ZN B 603 1555 1555 2.29 LINK SG CYS B 425 ZN ZN B 603 1555 1555 2.35 LINK SG CYS B 434 ZN ZN B 604 1555 1555 2.13 LINK SG CYS B 437 ZN ZN B 604 1555 1555 2.37 LINK SG CYS B 448 ZN ZN B 604 1555 1555 2.31 LINK SG CYS B 451 ZN ZN B 604 1555 1555 2.40 LINK O1B ADP B 601 MG MG B 602 1555 1555 2.98 CRYST1 44.415 74.449 109.400 84.66 80.03 82.77 P 1 2 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 0.022515 -0.002857 -0.003760 0.00000 SCALE2 0.000000 0.013540 -0.000991 0.00000 SCALE3 0.000000 0.000000 0.009306 0.00000