HEADER ENDONUCLEASE 15-SEP-92 1ABK OBSLTE 15-OCT-95 1ABK 2ABK TITLE ATOMIC STRUCTURE OF THE /DNA$ REPAIR [4*FE-4*S] ENZYME TITLE 2 ENDONUCLEASE /III$ COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS ENDONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR C.-F.KUO,D.E.MCREE,J.A.TAINER REVDAT 2 15-JAN-95 1ABK 1 COMPND REVDAT 1 15-JUL-93 1ABK 0 JRNL AUTH C.-F.KUO,D.E.MCREE,C.L.FISHER,S.O'HANDLEY, JRNL AUTH 2 R.P.CUNNINGHAM,J.A.TAINER JRNL TITL ATOMIC STRUCTURE OF THE /DNA REPAIR [4FE-4S] JRNL TITL 2 ENZYME ENDONUCLEASE /III JRNL REF SCIENCE V. 258 434 1992 JRNL REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.-F.KUO,D.E.MCREE,R.P.CUNNINGHAM,J.A.TAINER REMARK 1 TITL CRYSTALLIZATION AND CRYSTALLOGRAPHIC REMARK 1 TITL 2 CHARACTERIZATION OF THE IRON-SULFUR CONTAINING REMARK 1 TITL 3 DNA-REPAIR ENZYME ENDONUCLEASE III FROM REMARK 1 TITL 4 ESCHERICHIA COLI REMARK 1 REF J.MOL.BIOL. V. 227 347 1992 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR 1ABK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1652 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ABK COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1ABK THIS MOLECULE HAS A TWO DOMAIN STRUCTURE: 1ABK 1ABK A. REMARK 5 SIX HELIX BARREL DOMAIN CONSISTS OF RESIDUES 22 - 132 1ABK REMARK 5 WITH ALL SHORT +1 HELIX NEIGHBOR CONNECTIONS. 1ABK 1ABK B. REMARK 5 THE 4FE - 4S CLUSTER DOMAIN CONSISTS OF RESIDUES 1 - 1ABK REMARK 5 21 AND RESIDUES 133 - 211 WITH FOUR HELICES HAVING TWO 1ABK REMARK 5 GREEK KEY CONNECTIONS AND C-TERMINAL [4FE-4S] BINDING 1ABK REMARK 5 LOOP. 1ABK REMARK 6 REMARK 6 1ABK THERE IS A UNIQUE SHORT, SEQUENCE-CONTINUOUS [4FE-4S] REMARK 6 1ABK CLUSTER BINDING LOOP WITH LIGATION PATTERN CYS-X6-CYS- REMARK 6 X2- 1ABK CYS-X5-CYS. 1ABK REMARK 7 REMARK 7 1ABK HELIX E, F-G LOOP, HELIX H, AND [4FE-4S] CLUSTER LOOP REMARK 7 ARE 1ABK IMPLICATED IN DNA BINDING. 1ABK REMARK 8 REMARK 8 1ABK CORRECTION. CORRECT E.C. CODE ON COMPND RECORD. 1ABK REMARK 8 15-JAN-95. 1ABK REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-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 SMTRY1 2 -1.000000 0.000000 0.000000 24.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.90000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 VAL 209 CG1 CG2 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL 117 CA VAL 117 CB 0.092 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL 209 N - CA - C ANGL. DEV. = 17.7 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 LYS 206 -107.32 58.33 SEQRES 1 211 MET ASN LYS ALA LYS ARG LEU GLU ILE LEU THR ARG LEU SEQRES 2 211 ARG GLU ASN ASN PRO HIS PRO THR THR GLU LEU ASN PHE SEQRES 3 211 SER SER PRO PHE GLU LEU LEU ILE ALA VAL LEU LEU SER SEQRES 4 211 ALA GLN ALA THR ASP VAL SER VAL ASN LYS ALA THR ALA SEQRES 5 211 LYS LEU TYR PRO VAL ALA ASN THR PRO ALA ALA MET LEU SEQRES 6 211 GLU LEU GLY VAL GLU GLY VAL LYS THR TYR ILE LYS THR SEQRES 7 211 ILE GLY LEU TYR ASN SER LYS ALA GLU ASN ILE ILE LYS SEQRES 8 211 THR CYS ARG ILE LEU LEU GLU GLN HIS ASN GLY GLU VAL SEQRES 9 211 PRO GLU ASP ARG ALA ALA LEU GLU ALA LEU PRO GLY VAL SEQRES 10 211 GLY ARG LYS THR ALA ASN VAL VAL LEU ASN THR ALA PHE SEQRES 11 211 GLY TRP PRO THR ILE ALA VAL ASP THR HIS ILE PHE ARG SEQRES 12 211 VAL CYS ASN ARG THR GLN PHE ALA PRO GLY LYS ASN VAL SEQRES 13 211 GLU GLN VAL GLU GLU LYS LEU LEU LYS VAL VAL PRO ALA SEQRES 14 211 GLU PHE LYS VAL ASP CYS HIS HIS TRP LEU ILE LEU HIS SEQRES 15 211 GLY ARG TYR THR CYS ILE ALA ARG LYS PRO ARG CYS GLY SEQRES 16 211 SER CYS ILE ILE GLU ASP LEU CYS GLU TYR LYS GLU LYS SEQRES 17 211 VAL ASP ILE HET FS4 300 8 HETNAM FS4 IRON/SULFUR CLUSTER FORMUL 2 FS4 FE4 S4 FORMUL 3 HOH *118(H2 O1) HELIX 1 A LYS 3 ASN 16 1 14 HELIX 2 B PRO 29 SER 39 1 11 HELIX 3 C ASP 44 PRO 56 1 13 HELIX 4 D1 PRO 61 LEU 67 1 7 HELIX 5 D2 VAL 69 TYR 75 1 7 HELIX 6 E TYR 82 GLN 99 1 18 HELIX 7 F ASP 107 ALA 113 1 7 HELIX 8 G ARG 119 ALA 129 1 11 HELIX 9 H ASP 138 THR 148 1 11 HELIX 10 I VAL 156 VAL 166 1 11 HELIX 11 J CYS 175 TYR 185 1 11 TURN 1 FG LEU 114 VAL 117 ALPHA F TO ALPHA G TURN SITE 1 FES 4 CYS 187 CYS 194 CYS 197 CYS 203 CRYST1 48.500 65.800 86.800 90.00 90.00 90.00 P 21 21 21 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 0.020619 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011521 0.00000