HEADER HYDROLASE/DNA 21-JAN-08 3C0X TITLE I-SCEI IN COMPLEX WITH A TOP NICKED DNA SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)-3'); COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: DNA TOP STRAND B; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)- COMPND 9 3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA TOP STRAND C; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DCP COMPND 16 *DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: DNA BOTTOM STRAND D; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: INTRON-ENCODED ENDONUCLEASE I-SCEI; COMPND 22 CHAIN: A; COMPND 23 SYNONYM: 21S RRNA INTRON MATURASE, HOMING ENDONUCLEASE OMEGA; COMPND 24 EC: 3.1.-.-; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA SYNTHETIC PRODUCT; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: DNA SYNTHETIC PRODUCT; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: DNA SYNTHETIC PRODUCT; SOURCE 10 MOL_ID: 4; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 GENE: SCEI, OMEGA, SECY; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PET15 KEYWDS ENDONUCLEASE, HOMING, LADLIDADG, CATALYTIC MECHANISM, METAL BINDING, KEYWDS 2 NICKED INTERMEDIATE, HYDROLASE, INTRON HOMING, MITOCHONDRION, MRNA KEYWDS 3 PROCESSING, MRNA SPLICING, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.M.MOURE,F.S.GIMBLE,F.A.QUIOCHO REVDAT 4 30-AUG-23 3C0X 1 REMARK LINK REVDAT 3 24-FEB-09 3C0X 1 VERSN REVDAT 2 08-JUL-08 3C0X 1 JRNL REVDAT 1 06-MAY-08 3C0X 0 JRNL AUTH C.M.MOURE,F.S.GIMBLE,F.A.QUIOCHO JRNL TITL CRYSTAL STRUCTURES OF I-SCEI COMPLEXED TO NICKED DNA JRNL TITL 2 SUBSTRATES: SNAPSHOTS OF INTERMEDIATES ALONG THE DNA JRNL TITL 3 CLEAVAGE REACTION PATHWAY. JRNL REF NUCLEIC ACIDS RES. V. 36 3287 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18424798 JRNL DOI 10.1093/NAR/GKN178 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 18872 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) : 0.255 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 922 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 53 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 : 1854 REMARK 3 NUCLEIC ACID ATOMS : 979 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 58 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) : 3.43700 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 3.43700 REMARK 3 B13 (A**2) : -6.87300 REMARK 3 B23 (A**2) : 0.00000 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.320 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 3C0X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19007 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.05200 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43600 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1R7M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-26% 2-METHYL-2,4-PENTANEDIOL (MPD) REMARK 280 (V/V), 20 MM CACL2, 1 MM DITHIOTHREITOL, 100 MM SODIUM ACETATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 64.16000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.34000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.34000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.08000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.34000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.34000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 96.24000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.34000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.34000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.08000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.34000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.34000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 96.24000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.16000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7820 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D, 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 DC B 1 REMARK 465 DG D 1 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASN A 226 REMARK 465 THR A 227 REMARK 465 ILE A 228 REMARK 465 SER A 229 REMARK 465 SER A 230 REMARK 465 GLU A 231 REMARK 465 THR A 232 REMARK 465 PHE A 233 REMARK 465 LEU A 234 REMARK 465 LYS A 235 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 DA B 2 P OP1 OP2 REMARK 470 DG D 2 P OP1 OP2 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 DC C 15 P DC C 15 OP3 -0.094 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 MET A 10 26.80 -72.80 REMARK 500 ASN A 11 -3.52 -151.48 REMARK 500 GLN A 33 -35.68 -39.20 REMARK 500 ASP A 51 -146.44 -94.66 REMARK 500 ASP A 76 -66.99 -27.61 REMARK 500 PRO A 125 152.26 -47.08 REMARK 500 GLN A 219 23.08 -70.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA B 14 0.06 SIDE CHAIN REMARK 500 DA D 7 0.07 SIDE CHAIN REMARK 500 DA D 15 0.06 SIDE CHAIN REMARK 500 DA D 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 HETATOM RENUMBERING REMARK 600 CA 1-3 IN PUBLICATION CORRESPONDS TO CA 301-303 IN THE REMARK 600 PDB FILE. HOH 1-58 IN PUBLICATION CORRESPONDS TO HOH REMARK 600 401-458 IN THE PDB FILE. THE PUTATIVE NUCLEOPHILIC WATER REMARK 600 28 IN PUBLICATION CORRESPONDS TO HOH A428 IN THE PDB FILE. 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 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 14 OP1 REMARK 620 2 DC D 17 OP1 98.3 REMARK 620 3 HOH D 435 O 91.9 62.4 REMARK 620 4 ASP A 44 OD2 93.2 113.5 173.9 REMARK 620 5 ASP A 144 O 173.8 86.9 93.5 81.6 REMARK 620 6 HOH A 428 O 90.4 155.0 94.0 89.2 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 15 OP3 REMARK 620 2 HOH C 433 O 72.4 REMARK 620 3 DT D 16 OP1 102.4 158.6 REMARK 620 4 HOH D 412 O 92.0 84.3 75.1 REMARK 620 5 HOH D 432 O 154.6 82.3 102.0 87.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 17 OP2 REMARK 620 2 ASP A 44 OD1 89.3 REMARK 620 3 ASP A 145 OD1 73.9 80.0 REMARK 620 4 HOH A 425 O 143.0 125.5 98.0 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 CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R7M RELATED DB: PDB REMARK 900 I-SCEI DNA COMPLEX REMARK 900 RELATED ID: 3COW RELATED DB: PDB REMARK 900 I-SCEI BOTTON NICKED DNA SUBSTRATE STRUCTURE DBREF 3C0X A 1 235 UNP P03882 SCE1_YEAST 1 235 DBREF 3C0X B 1 14 PDB 3C0X 3C0X 1 14 DBREF 3C0X C 15 25 PDB 3C0X 3C0X 15 25 DBREF 3C0X D 1 25 PDB 3C0X 3C0X 1 25 SEQRES 1 B 14 DC DA DC DG DC DT DA DG DG DG DA DT DA SEQRES 2 B 14 DA SEQRES 1 C 11 DC DA DG DG DG DT DA DA DT DA DC SEQRES 1 D 25 DG DG DT DA DT DT DA DC DC DC DT DG DT SEQRES 2 D 25 DT DA DT DC DC DC DT DA DG DC DG DT SEQRES 1 A 235 MET LYS ASN ILE LYS LYS ASN GLN VAL MET ASN LEU GLY SEQRES 2 A 235 PRO ASN SER LYS LEU LEU LYS GLU TYR LYS SER GLN LEU SEQRES 3 A 235 ILE GLU LEU ASN ILE GLU GLN PHE GLU ALA GLY ILE GLY SEQRES 4 A 235 LEU ILE LEU GLY ASP ALA TYR ILE ARG SER ARG ASP GLU SEQRES 5 A 235 GLY LYS THR TYR CYS MET GLN PHE GLU TRP LYS ASN LYS SEQRES 6 A 235 ALA TYR MET ASP HIS VAL CYS LEU LEU TYR ASP GLN TRP SEQRES 7 A 235 VAL LEU SER PRO PRO HIS LYS LYS GLU ARG VAL ASN HIS SEQRES 8 A 235 LEU GLY ASN LEU VAL ILE THR TRP GLY ALA GLN THR PHE SEQRES 9 A 235 LYS HIS GLN ALA PHE ASN LYS LEU ALA ASN LEU PHE ILE SEQRES 10 A 235 VAL ASN ASN LYS LYS THR ILE PRO ASN ASN LEU VAL GLU SEQRES 11 A 235 ASN TYR LEU THR PRO MET SER LEU ALA TYR TRP PHE MET SEQRES 12 A 235 ASP ASP GLY GLY LYS TRP ASP TYR ASN LYS ASN SER THR SEQRES 13 A 235 ASN LYS SER ILE VAL LEU ASN THR GLN SER PHE THR PHE SEQRES 14 A 235 GLU GLU VAL GLU TYR LEU VAL LYS GLY LEU ARG ASN LYS SEQRES 15 A 235 PHE GLN LEU ASN CYS TYR VAL LYS ILE ASN LYS ASN LYS SEQRES 16 A 235 PRO ILE ILE TYR ILE ASP SER MET SER TYR LEU ILE PHE SEQRES 17 A 235 TYR ASN LEU ILE LYS PRO TYR LEU ILE PRO GLN MET MET SEQRES 18 A 235 TYR LYS LEU PRO ASN THR ILE SER SER GLU THR PHE LEU SEQRES 19 A 235 LYS HET CA C 302 1 HET CA A 301 1 HET CA A 303 1 HETNAM CA CALCIUM ION FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *58(H2 O) HELIX 1 1 LYS A 5 MET A 10 1 6 HELIX 2 2 SER A 16 LEU A 26 1 11 HELIX 3 3 ASN A 30 GLY A 43 1 14 HELIX 4 4 ASN A 64 TYR A 75 1 12 HELIX 5 5 ASP A 76 VAL A 79 5 4 HELIX 6 6 HIS A 106 ALA A 108 5 3 HELIX 7 7 PHE A 109 ASN A 114 1 6 HELIX 8 8 ASN A 127 LEU A 133 1 7 HELIX 9 9 THR A 134 ASP A 145 1 12 HELIX 10 10 THR A 168 GLN A 184 1 17 HELIX 11 11 SER A 204 LYS A 213 1 10 HELIX 12 12 ILE A 217 LEU A 224 5 8 SHEET 1 A 4 TYR A 46 ARG A 48 0 SHEET 2 A 4 CYS A 57 TRP A 62 -1 O GLN A 59 N TYR A 46 SHEET 3 A 4 LEU A 95 GLN A 102 -1 O ALA A 101 N PHE A 60 SHEET 4 A 4 HIS A 84 VAL A 89 -1 N LYS A 86 O THR A 98 SHEET 1 B 2 ILE A 117 VAL A 118 0 SHEET 2 B 2 LYS A 121 LYS A 122 -1 O LYS A 121 N VAL A 118 SHEET 1 C 4 GLY A 146 LYS A 148 0 SHEET 2 C 4 ILE A 160 LEU A 162 -1 O VAL A 161 N GLY A 147 SHEET 3 C 4 LYS A 195 ILE A 200 -1 O ILE A 198 N LEU A 162 SHEET 4 C 4 CYS A 187 ASN A 192 -1 N TYR A 188 O TYR A 199 LINK OP1 DA B 14 CA CA A 301 1555 1555 2.24 LINK OP3 DC C 15 CA CA C 302 1555 1555 2.27 LINK CA CA C 302 O HOH C 433 1555 1555 2.20 LINK CA CA C 302 OP1 DT D 16 1555 1555 2.51 LINK CA CA C 302 O HOH D 412 1555 1555 2.67 LINK CA CA C 302 O HOH D 432 1555 1555 2.04 LINK OP1 DC D 17 CA CA A 301 1555 1555 2.51 LINK OP2 DC D 17 CA CA A 303 1555 1555 2.18 LINK O HOH D 435 CA CA A 301 1555 1555 2.15 LINK OD2 ASP A 44 CA CA A 301 1555 1555 2.38 LINK OD1 ASP A 44 CA CA A 303 1555 1555 2.37 LINK O ASP A 144 CA CA A 301 1555 1555 2.29 LINK OD1 ASP A 145 CA CA A 303 1555 1555 2.07 LINK CA CA A 301 O HOH A 428 1555 1555 2.37 LINK CA CA A 303 O HOH A 425 1555 1555 2.87 SITE 1 AC1 6 ASP A 44 ASP A 144 HOH A 428 DA B 14 SITE 2 AC1 6 DC D 17 HOH D 435 SITE 1 AC2 6 DC C 15 HOH C 433 DA D 15 DT D 16 SITE 2 AC2 6 HOH D 412 HOH D 432 SITE 1 AC3 8 GLY A 43 ASP A 44 ASP A 145 HOH A 425 SITE 2 AC3 8 HOH A 442 DA B 14 DC C 15 DC D 17 CRYST1 80.680 80.680 128.320 90.00 90.00 90.00 P 41 21 2 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 0.012395 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012395 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007793 0.00000