HEADER GENE REGULATION/DNA 23-APR-99 1CKT TITLE CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA TITLE 2 DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*(5IU) COMPND 3 P*CP*TP*CP*TP*GP*GP*AP*CP*CP*TP*TP*CP*C)-3'); COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*AP*GP*G)- COMPND 8 3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HIGH MOBILITY GROUP 1 PROTEIN; COMPND 13 CHAIN: A; COMPND 14 FRAGMENT: RESIDUES 8-78, DOMAIN A; COMPND 15 SYNONYM: HMG-1, AMPHOTERIN, HEPARIN-BINDING PROTEIN P30; COMPND 16 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: RATTUS NORVEGICUS; SOURCE 7 ORGANISM_COMMON: NORWAY RAT; SOURCE 8 ORGANISM_TAXID: 10116; SOURCE 9 STRAIN: SORAGYE-DAWLEY; SOURCE 10 TISSUE: LIVER; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PT7-HMG1BA; SOURCE 15 EXPRESSION_SYSTEM_GENE: HMG1 DOMAIN A (M1-F89) KEYWDS HIGH-MOBILITY GROUP DOMAIN, BENT DNA, PROTEIN-DRUG-DNA COMPLEX, GENE KEYWDS 2 REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR U.-M.OHNDORF,M.A.ROULD,C.O.PABO,S.J.LIPPARD REVDAT 7 27-DEC-23 1CKT 1 REMARK LINK REVDAT 6 13-JUL-11 1CKT 1 VERSN REVDAT 5 23-JUN-10 1CKT 1 FORMUL REVDAT 4 24-FEB-09 1CKT 1 VERSN REVDAT 3 01-APR-03 1CKT 1 JRNL REVDAT 2 18-DEC-99 1CKT 1 JRNL REVDAT 1 30-JUN-99 1CKT 0 JRNL AUTH U.M.OHNDORF,M.A.ROULD,Q.HE,C.O.PABO,S.J.LIPPARD JRNL TITL BASIS FOR RECOGNITION OF CISPLATIN-MODIFIED DNA BY JRNL TITL 2 HIGH-MOBILITY-GROUP PROTEINS. JRNL REF NATURE V. 399 708 1999 JRNL REFN ISSN 0028-0836 JRNL PMID 10385126 JRNL DOI 10.1038/21460 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 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) (%) : 65.6 REMARK 3 NUMBER OF REFLECTIONS : 17638 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) : 0.238 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1710 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 : 562 REMARK 3 NUCLEIC ACID ATOMS : 650 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 74 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 32.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 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: REMARK 3 TYR: TYR 77 C-TERMINAL OXYGEN OXT WAS NOT FOUND IN ELECTRON REMARK 3 DENSITY MAP; C-TERMINAL RESIDUES 78-89 WERE NOT SEEN IN DENSITY MAP REMARK 4 REMARK 4 1CKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9655 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04400 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED FROM A SOLUTION REMARK 280 THAT CONTAINED HEPES, MAGNESIUM ACETATE, PEG 3350, GLYCEROL AND REMARK 280 DTT, PH 6.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 52.60500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.60500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.20500 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 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 LYS A 7 CG CD CE NZ REMARK 470 ARG A 9 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LYS A 29 CD CE NZ REMARK 470 HIS A 30 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 32 CG OD1 OD2 REMARK 470 SER A 34 OG REMARK 470 LYS A 64 CG CD CE NZ 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 PRO A 31 10.26 -69.69 REMARK 500 ALA A 33 116.83 -20.80 REMARK 500 VAL A 35 101.27 67.37 REMARK 500 ALA A 53 -24.57 -39.60 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 DC B 101 0.06 SIDE CHAIN REMARK 500 DG C 215 0.09 SIDE CHAIN 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 CPT B 99 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 108 N7 REMARK 620 2 CPT B 99 N1 177.3 REMARK 620 3 CPT B 99 N2 88.7 89.1 REMARK 620 4 DG B 108 C8 28.1 153.7 91.4 REMARK 620 5 DG B 108 C5 14.5 164.6 94.3 41.4 REMARK 620 6 DG B 109 N7 90.3 92.0 176.1 86.0 85.6 REMARK 620 7 DG B 109 C8 90.0 92.7 150.7 74.5 91.7 25.5 REMARK 620 8 DG B 109 C5 91.5 90.3 166.8 95.0 83.1 17.0 42.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT B 99 DBREF 1CKT A 7 77 UNP P63159 HMG1_RAT 7 77 DBREF 1CKT B 101 116 PDB 1CKT 1CKT 101 116 DBREF 1CKT C 201 216 PDB 1CKT 1CKT 201 216 SEQRES 1 B 16 DC DC 5IU DC DT DC DT DG DG DA DC DC DT SEQRES 2 B 16 DT DC DC SEQRES 1 C 16 DG DG DA DA DG DG DT DC DC DA DG DA DG SEQRES 2 C 16 DA DG DG SEQRES 1 A 71 LYS PRO ARG GLY LYS MET SER SER TYR ALA PHE PHE VAL SEQRES 2 A 71 GLN THR CYS ARG GLU GLU HIS LYS LYS LYS HIS PRO ASP SEQRES 3 A 71 ALA SER VAL ASN PHE SER GLU PHE SER LYS LYS CYS SER SEQRES 4 A 71 GLU ARG TRP LYS THR MET SER ALA LYS GLU LYS GLY LYS SEQRES 5 A 71 PHE GLU ASP MET ALA LYS ALA ASP LYS ALA ARG TYR GLU SEQRES 6 A 71 ARG GLU MET LYS THR TYR MODRES 1CKT 5IU B 103 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HET 5IU B 103 20 HET CPT B 99 3 HETNAM 5IU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM CPT CISPLATIN HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 1 5IU C9 H12 I N2 O8 P FORMUL 4 CPT CL2 H6 N2 PT FORMUL 5 HOH *74(H2 O) HELIX 1 1 SER A 14 LYS A 29 1 16 HELIX 2 2 PHE A 37 LYS A 49 1 13 HELIX 3 3 GLY A 57 MET A 74 1 18 LINK O3' DC B 102 P 5IU B 103 1555 1555 1.59 LINK O3' 5IU B 103 P DC B 104 1555 1555 1.60 LINK PT1 CPT B 99 N7 DG B 108 1555 1555 1.94 LINK PT1 CPT B 99 C8 DG B 108 1555 1555 2.64 LINK PT1 CPT B 99 C5 DG B 108 1555 1555 3.18 LINK PT1 CPT B 99 N7 DG B 109 1555 1555 1.89 LINK PT1 CPT B 99 C8 DG B 109 1555 1555 2.73 LINK PT1 CPT B 99 C5 DG B 109 1555 1555 3.09 SITE 1 AC1 2 DG B 108 DG B 109 CRYST1 105.210 50.410 53.130 90.00 99.82 90.00 C 1 2 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 0.009505 0.000000 0.001645 0.00000 SCALE2 0.000000 0.019837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019102 0.00000