HEADER HYDROLASE/DNA 14-MAR-03 1ORP TITLE STRUCTURE OF A TRAPPED ENDONUCLEASE III-DNA COVALENT INTERMEDIATE: TITLE 2 ESTRANGED-ADENINE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*GP*AP*CP*AP*TP*GP*GP*AP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ENDONUCLEASE III; COMPND 11 CHAIN: A; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 7 ORGANISM_TAXID: 1422; SOURCE 8 GENE: NTH; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(C41); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS DNA REPAIR, DNA GLYCOSYLASE, [4FE-4S] CLUSTER, IRON-SULFUR CLUSTER, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.C.FROMME,G.L.VERDINE REVDAT 5 20-NOV-24 1ORP 1 REMARK REVDAT 4 16-AUG-23 1ORP 1 REMARK LINK REVDAT 3 31-MAR-09 1ORP 1 ATOM CONECT REVDAT 2 24-FEB-09 1ORP 1 VERSN REVDAT 1 15-JUL-03 1ORP 0 JRNL AUTH J.C.FROMME,G.L.VERDINE JRNL TITL STRUCTURE OF A TRAPPED ENDONUCLEASE III-DNA COVALENT JRNL TITL 2 INTERMEDIATE JRNL REF EMBO J. V. 22 3461 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12840008 JRNL DOI 10.1093/EMBOJ/CDG311 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 570754.360 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 14943 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) : 0.241 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1190 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1275 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 104 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1579 REMARK 3 NUCLEIC ACID ATOMS : 416 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68000 REMARK 3 B22 (A**2) : -15.11000 REMARK 3 B33 (A**2) : 14.43000 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) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.34 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 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) : 1.350 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.100 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.140 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 74.61 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : PED_FS4.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : PED_FS4.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ORP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9363 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15614 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1ORN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, TRIS, BETA-MERCAPTOETHANOL , REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 33.86600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.25800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.86600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.25800 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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 DT C 12 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 LYS A 214 REMARK 465 ARG A 215 REMARK 465 GLU A 216 REMARK 465 GLU A 217 REMARK 465 LYS A 218 REMARK 465 ALA A 219 REMARK 465 ALA A 220 REMARK 465 ASN A 221 REMARK 465 GLN A 222 REMARK 465 LYS A 223 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 DG C 13 P OP1 OP2 REMARK 470 MET A 1 CG SD CE REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 ILE A 7 CG1 CG2 CD1 REMARK 470 ARG A 8 NE CZ NH1 NH2 REMARK 470 LYS A 16 CE NZ REMARK 470 ASP A 20 CB CG OD1 OD2 REMARK 470 ARG A 28 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 ARG A 54 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 57 CB CG CD OE1 OE2 REMARK 470 ARG A 60 CD NE CZ NH1 NH2 REMARK 470 GLU A 71 CB CG CD OE1 OE2 REMARK 470 GLN A 75 CB CG CD OE1 NE2 REMARK 470 ARG A 78 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 88 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 92 CD CE NZ REMARK 470 LYS A 100 CD CE NZ REMARK 470 GLU A 104 CD OE1 OE2 REMARK 470 ARG A 153 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 GLU A 160 CG CD OE1 OE2 REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 LYS A 171 CE NZ REMARK 470 GLU A 172 CG CD OE1 OE2 REMARK 470 LYS A 190 CB CG CD CE NZ REMARK 470 GLN A 192 CB CG CD OE1 NE2 REMARK 470 SER A 193 CB OG REMARK 470 SER A 198 CB OG REMARK 470 LEU A 202 CG CD1 CD2 REMARK 470 ARG A 206 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 209 CE NZ REMARK 470 LYS A 210 CG CD CE NZ REMARK 470 ARG A 211 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 213 CG CD NE CZ NH1 NH2 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 ARG A 60 -9.51 -140.56 REMARK 500 ASP A 139 -166.21 -113.52 REMARK 500 LYS A 171 -39.86 -32.01 REMARK 500 HIS A 188 -75.40 -134.71 REMARK 500 LEU A 204 12.80 -142.94 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 NA A 224 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 21 OP1 REMARK 620 2 HOH C 34 O 83.9 REMARK 620 3 MET A 113 O 163.8 80.0 REMARK 620 4 LEU A 115 O 92.4 170.2 103.6 REMARK 620 5 VAL A 118 O 90.7 72.0 84.7 99.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 300 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 189 SG REMARK 620 2 SF4 A 300 S1 103.3 REMARK 620 3 SF4 A 300 S3 115.0 107.9 REMARK 620 4 SF4 A 300 S4 124.8 98.5 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 300 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 196 SG REMARK 620 2 SF4 A 300 S1 107.2 REMARK 620 3 SF4 A 300 S2 125.5 103.7 REMARK 620 4 SF4 A 300 S4 107.7 104.6 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 300 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 199 SG REMARK 620 2 SF4 A 300 S2 118.8 REMARK 620 3 SF4 A 300 S3 118.7 99.9 REMARK 620 4 SF4 A 300 S4 116.0 100.8 99.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 300 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 SF4 A 300 S1 117.1 REMARK 620 3 SF4 A 300 S2 108.4 100.9 REMARK 620 4 SF4 A 300 S3 118.3 103.6 106.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ABK RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI ENDONUCLEASE III WITHOUT DNA REMARK 900 RELATED ID: 1ORN RELATED DB: PDB REMARK 900 STRUCTURE OF A TRAPPED ENDONUCLEASE III - DNA COVALENT INTERMEDIATE: REMARK 900 ESTRANGED-GUANINE COMPLEX REMARK 999 REMARK 999 AUTHORS INFORMED THAT THE SEQUENCE OF THE PROTEIN HAS NOT REMARK 999 YET BEEN PUBLISHED. RESIDUES GLY -2, SER -1 AND HIS 0 ARE REMARK 999 CLONING ARTIFACTS. DBREF 1ORP B 1 11 PDB 1ORP 1ORP 1 11 DBREF 1ORP C 12 22 PDB 1ORP 1ORP 12 22 DBREF 1ORP A -2 223 PDB 1ORP 1ORP -2 223 SEQRES 1 B 11 DA DA DG DA DC DA DT DG DG DA DC SEQRES 1 C 11 DT DG DT DC DC DA PED DG DT DC DT SEQRES 1 A 226 GLY SER HIS MET LEU THR LYS GLN GLN ILE ARG TYR CYS SEQRES 2 A 226 LEU ASP GLU MET ALA LYS MET PHE PRO ASP ALA HIS CYS SEQRES 3 A 226 GLU LEU VAL HIS ARG ASN PRO PHE GLU LEU LEU ILE ALA SEQRES 4 A 226 VAL VAL LEU SER ALA GLN CYS THR ASP ALA LEU VAL ASN SEQRES 5 A 226 LYS VAL THR LYS ARG LEU PHE GLU LYS TYR ARG THR PRO SEQRES 6 A 226 HIS ASP TYR ILE ALA VAL PRO LEU GLU GLU LEU GLU GLN SEQRES 7 A 226 ASP ILE ARG SER ILE GLY LEU TYR ARG ASN LYS ALA ARG SEQRES 8 A 226 ASN ILE GLN LYS LEU CYS ALA MET LEU ILE ASP LYS TYR SEQRES 9 A 226 ASN GLY GLU VAL PRO ARG ASP ARG ASP GLU LEU MET LYS SEQRES 10 A 226 LEU PRO GLY VAL GLY ARG LYS THR ALA ASN VAL VAL VAL SEQRES 11 A 226 SER VAL ALA PHE GLY VAL PRO ALA ILE ALA VAL ASP THR SEQRES 12 A 226 HIS VAL GLU ARG VAL SER LYS ARG LEU GLY PHE CYS ARG SEQRES 13 A 226 TRP ASP ASP SER VAL LEU GLU VAL GLU LYS THR LEU MET SEQRES 14 A 226 LYS ILE ILE PRO LYS GLU GLU TRP SER ILE THR HIS HIS SEQRES 15 A 226 ARG MET ILE PHE PHE GLY ARG TYR HIS CYS LYS ALA GLN SEQRES 16 A 226 SER PRO GLN CYS PRO SER CYS PRO LEU LEU HIS LEU CYS SEQRES 17 A 226 ARG GLU GLY LYS LYS ARG MET ARG LYS ARG GLU GLU LYS SEQRES 18 A 226 ALA ALA ASN GLN LYS HET PED C 18 11 HET NA A 224 1 HET SF4 A 300 8 HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETNAM NA SODIUM ION HETNAM SF4 IRON/SULFUR CLUSTER HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE FORMUL 2 PED C5 H13 O6 P FORMUL 4 NA NA 1+ FORMUL 5 SF4 FE4 S4 FORMUL 6 HOH *71(H2 O) HELIX 1 1 THR A 3 PHE A 18 1 16 HELIX 2 2 ASN A 29 SER A 40 1 12 HELIX 3 3 THR A 44 TYR A 59 1 16 HELIX 4 4 THR A 61 VAL A 68 1 8 HELIX 5 5 PRO A 69 ILE A 77 1 9 HELIX 6 6 LEU A 82 TYR A 101 1 20 HELIX 7 7 ASP A 108 MET A 113 1 6 HELIX 8 8 GLY A 119 GLY A 132 1 14 HELIX 9 9 ASP A 139 LEU A 149 1 11 HELIX 10 10 SER A 157 ILE A 169 1 13 HELIX 11 12 GLU A 173 HIS A 188 1 16 HELIX 12 13 GLN A 195 CYS A 199 5 5 HELIX 13 14 LEU A 201 LEU A 204 5 4 HELIX 14 15 CYS A 205 ARG A 213 1 9 LINK O3' DA C 17 P PED C 18 1555 1555 1.60 LINK O3' PED C 18 P DG C 19 1555 1555 1.61 LINK C1' PED C 18 NZ LYS A 121 1555 1555 1.47 LINK OP1 DC C 21 NA NA A 224 1555 1555 2.48 LINK O HOH C 34 NA NA A 224 1555 1555 2.91 LINK O MET A 113 NA NA A 224 1555 1555 2.31 LINK O LEU A 115 NA NA A 224 1555 1555 2.43 LINK O VAL A 118 NA NA A 224 1555 1555 2.52 LINK SG CYS A 189 FE2 SF4 A 300 1555 1555 2.62 LINK SG CYS A 196 FE3 SF4 A 300 1555 1555 2.67 LINK SG CYS A 199 FE1 SF4 A 300 1555 1555 2.39 LINK SG CYS A 205 FE4 SF4 A 300 1555 1555 2.42 SITE 1 AC1 5 MET A 113 LEU A 115 VAL A 118 DC C 21 SITE 2 AC1 5 HOH C 34 SITE 1 AC2 7 LEU A 149 PHE A 184 CYS A 189 CYS A 196 SITE 2 AC2 7 CYS A 199 CYS A 205 GLY A 208 CRYST1 67.732 106.516 41.661 90.00 90.00 90.00 P 21 21 2 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 0.014764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024003 0.00000