PDB Short entry for 1QRV HEADER GENE REGULATION/DNA 15-JUN-99 1QRV TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HIGH MOBILITY GROUP PROTEIN D; COMPND 7 CHAIN: A, B; COMPND 8 FRAGMENT: RESIDUES 2-74; COMPND 9 SYNONYM: HMG-D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 5 ORGANISM_COMMON: FRUIT FLY; SOURCE 6 ORGANISM_TAXID: 7227; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET13A KEYWDS PROTEIN-DNA COMPLEX, HMG DOMAIN, NON-SEQUENCE SPECIFIC CHROMOSOMAL KEYWDS 2 PROTEIN HMG-D, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.V.MURPHY IV,R.M.SWEET,M.E.A.CHURCHILL REVDAT 7 14-FEB-24 1QRV 1 REMARK REVDAT 6 31-JAN-18 1QRV 1 JRNL REVDAT 5 24-FEB-09 1QRV 1 VERSN REVDAT 4 01-APR-03 1QRV 1 JRNL REVDAT 3 26-SEP-01 1QRV 1 HELIX REVDAT 2 07-JAN-00 1QRV 1 AUTHOR JRNL REVDAT 1 18-DEC-99 1QRV 0 JRNL AUTH F.V.MURPHY IV,R.M.SWEET,M.E.CHURCHILL JRNL TITL THE STRUCTURE OF A CHROMOSOMAL HIGH MOBILITY GROUP JRNL TITL 2 PROTEIN-DNA COMPLEX REVEALS SEQUENCE-NEUTRAL MECHANISMS JRNL TITL 3 IMPORTANT FOR NON-SEQUENCE-SPECIFIC DNA RECOGNITION. JRNL REF EMBO J. V. 18 6610 1999 JRNL REFN ISSN 0261-4189 JRNL PMID 10581235 JRNL DOI 10.1093/EMBOJ/18.23.6610 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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 : PROTEIN: ENGH & HUBER, DNA: PARKINSON ET AL. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 931772.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 10672 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 560 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1648 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87 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 : 1160 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.56000 REMARK 3 B22 (A**2) : -4.17000 REMARK 3 B33 (A**2) : -4.38000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 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) : 2.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.320 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.640 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 32.39 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.PA REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PA REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED CROSS VALIDATED MAXIMUM LIKELIHOOD REMARK 3 PROCEDURE INSTITUTED IN CNS 0.5. REMARK 4 REMARK 4 1QRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000009190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-98; 02-JUL-96 REMARK 200 TEMPERATURE (KELVIN) : 100.0; 100.0 REMARK 200 PH : 7.85 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : NSLS; ROTATING ANODE REMARK 200 BEAMLINE : X12C; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000,0.9211,0.92157,1.05; REMARK 200 1.5418 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4; RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10672 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.2000 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.19800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, TRIZMA-CL, NACL, PH 7.85, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K 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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.42150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.89850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.42150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.89850 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, 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 SER B 2 REMARK 465 GLY B 74 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 SER A 2 OG REMARK 470 LYS A 6 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA C 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LEF RELATED DB: PDB REMARK 900 RELATED PROTEIN LEF-1 COMPLEXED TO DNA SEQUENCE SPECIFIC NMR REMARK 900 RELATED ID: 1HRZ RELATED DB: PDB REMARK 900 RELATED PROTEIN SRY COMPLEXED TO DNA SEQUENCE SPECIFIC NMR REMARK 900 RELATED ID: 1HMA RELATED DB: PDB REMARK 900 RELATED PROTEIN HMG1 DOMAIN A FREE NMR REMARK 900 RELATED ID: 1HMF RELATED DB: PDB REMARK 900 RELATED PROTEIN HMG1 DOMAIN B FREE NMR REMARK 900 RELATED ID: 1CG7 RELATED DB: PDB REMARK 900 RELATED PROTEIN NHP6A REMARK 900 RELATED ID: 1CKT RELATED DB: PDB REMARK 900 RELATED PROTEIN HMG1 DOMAIN A BOUND TO CISPLATIN MODIFIED DNA DBREF 1QRV A 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 1QRV B 2 74 UNP Q05783 HMGD_DROME 2 74 DBREF 1QRV C 1 10 PDB 1QRV 1QRV 1 10 DBREF 1QRV D 11 20 PDB 1QRV 1QRV 11 20 SEQRES 1 C 10 DG DC DG DA DT DA DT DC DG DC SEQRES 1 D 10 DG DC DG DA DT DA DT DC DG DC SEQRES 1 A 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR MET LEU SEQRES 2 A 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 A 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 A 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 A 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 A 73 VAL LYS GLU PHE GLU ALA ASN GLY SEQRES 1 B 73 SER ASP LYS PRO LYS ARG PRO LEU SER ALA TYR MET LEU SEQRES 2 B 73 TRP LEU ASN SER ALA ARG GLU SER ILE LYS ARG GLU ASN SEQRES 3 B 73 PRO GLY ILE LYS VAL THR GLU VAL ALA LYS ARG GLY GLY SEQRES 4 B 73 GLU LEU TRP ARG ALA MET LYS ASP LYS SER GLU TRP GLU SEQRES 5 B 73 ALA LYS ALA ALA LYS ALA LYS ASP ASP TYR ASP ARG ALA SEQRES 6 B 73 VAL LYS GLU PHE GLU ALA ASN GLY HET NA C 501 1 HETNAM NA SODIUM ION FORMUL 5 NA NA 1+ FORMUL 6 HOH *116(H2 O) HELIX 1 1 SER A 10 GLU A 26 1 17 HELIX 2 2 LYS A 31 MET A 46 1 16 HELIX 3 3 LYS A 49 GLU A 71 1 23 HELIX 4 4 SER B 10 ASN B 27 1 18 HELIX 5 5 LYS B 31 MET B 46 1 16 HELIX 6 6 LYS B 49 ALA B 72 1 24 LINK OP1 DA C 6 NA NA C 501 1555 1555 2.78 SITE 1 AC1 1 DA C 6 CRYST1 43.740 53.797 86.843 90.00 90.00 90.00 P 21 21 21 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 0.022862 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011515 0.00000