PDB Short entry for 1BDT HEADER GENE REGULATION/DNA 11-MAY-98 1BDT TITLE WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)- COMPND 4 3'); COMPND 5 CHAIN: E; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP*TP*AP*T)- COMPND 10 3'); COMPND 11 CHAIN: F; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PROTEIN (GENE-REGULATING PROTEIN ARC); COMPND 15 CHAIN: A, B, C, D; 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: ENTEROBACTERIA PHAGE P22; SOURCE 7 ORGANISM_TAXID: 10754; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 OTHER_DETAILS: SYNTHETIC GENE KEYWDS GENE-REGULATING PROTEIN, GENE REGULATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.F.SCHILBACH,A.W.KARZAI,B.E.RAUMANN,R.T.SAUER REVDAT 5 02-AUG-23 1BDT 1 REMARK REVDAT 4 29-NOV-17 1BDT 1 HELIX REVDAT 3 24-FEB-09 1BDT 1 VERSN REVDAT 2 01-APR-03 1BDT 1 JRNL REVDAT 1 16-FEB-99 1BDT 0 JRNL AUTH J.F.SCHILDBACH,A.W.KARZAI,B.E.RAUMANN,R.T.SAUER JRNL TITL ORIGINS OF DNA-BINDING SPECIFICITY: ROLE OF PROTEIN CONTACTS JRNL TITL 2 WITH THE DNA BACKBONE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 811 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 9927650 JRNL DOI 10.1073/PNAS.96.3.811 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 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) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 12055 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) : 0.236 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.75 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 979 REMARK 3 BIN R VALUE (WORKING SET) : 0.4482 REMARK 3 BIN FREE R VALUE : 0.5140 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 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 : 1697 REMARK 3 NUCLEIC ACID ATOMS : 896 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 83 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.410 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.12 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.260 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 1BDT 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_1000171635. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12055 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.9 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 <I/SIGMA(I)> 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: X-PLOR REMARK 200 STARTING MODEL: 1PAR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.20500 REMARK 290 SMTRY3 2 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, A, B, C, D 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 ALA A 53 REMARK 465 ILE C 51 REMARK 465 GLY C 52 REMARK 465 ALA C 53 REMARK 465 ILE D 51 REMARK 465 GLY D 52 REMARK 465 ALA D 53 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 SER A 5 -32.25 165.27 REMARK 500 SER C 5 -5.58 -48.75 REMARK 500 PHE D 10 123.32 -178.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BDT A 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1BDT B 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1BDT C 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1BDT D 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1BDT E 1 22 PDB 1BDT 1BDT 1 22 DBREF 1BDT F 1 22 PDB 1BDT 1BDT 1 22 SEQRES 1 E 22 DT DA DT DA DG DT DA DG DA DG DT DG DC SEQRES 2 E 22 DT DT DC DT DA DT DC DA DT SEQRES 1 F 22 DA DA DT DG DA DT DA DG DA DA DG DC DA SEQRES 2 F 22 DC DT DC DT DA DC DT DA DT SEQRES 1 A 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG SEQRES 2 A 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 A 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 A 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 A 53 ALA SEQRES 1 B 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG SEQRES 2 B 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 B 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 B 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 B 53 ALA SEQRES 1 C 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG SEQRES 2 C 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 C 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 C 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 C 53 ALA SEQRES 1 D 53 MET LYS GLY MET SER LYS MET PRO GLN PHE ASN LEU ARG SEQRES 2 D 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 D 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 D 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 D 53 ALA FORMUL 7 HOH *83(H2 O) HELIX 1 A1 PRO A 15 GLY A 30 1 16 HELIX 2 B1 SER A 32 GLU A 48 1 17 HELIX 3 A2 PRO B 15 GLY B 30 1 16 HELIX 4 B2 SER B 32 GLU B 48 1 17 HELIX 5 A3 PRO C 15 GLY C 30 1 16 HELIX 6 B3 SER C 32 GLU C 48 1 17 HELIX 7 A4 PRO D 15 GLY D 30 1 16 HELIX 8 B4 SER D 32 GLU D 48 1 17 SHEET 1 AB 2 PRO A 8 TRP A 14 0 SHEET 2 AB 2 PRO B 8 TRP B 14 -1 O PHE B 10 N LEU A 12 SHEET 1 CD 2 PRO C 8 TRP C 14 0 SHEET 2 CD 2 PRO D 8 TRP D 14 -1 O PHE D 10 N LEU C 12 CRYST1 62.130 56.410 52.330 90.00 104.14 90.00 P 1 21 1 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 0.016095 0.000000 0.004055 0.00000 SCALE2 0.000000 0.017727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019707 0.00000 MTRIX1 1 -0.511800 0.112700 -0.851700 63.45470 1 MTRIX2 1 0.130700 -0.969600 -0.206800 -8.03550 1 MTRIX3 1 -0.849100 -0.217200 0.481500 35.21450 1 MTRIX1 2 0.535600 0.039500 -0.843500 58.08270 1 MTRIX2 2 0.042600 -0.998900 -0.019800 -4.33970 1 MTRIX3 2 -0.843400 -0.025300 -0.536700 105.34710 1 MTRIX1 3 0.014600 0.119900 -0.992700 70.37200 1 MTRIX2 3 0.100400 -0.987900 -0.117900 -5.90280 1 MTRIX3 3 -0.994800 -0.098000 -0.026400 71.22350 1