HEADER TRANSCRIPTION/DNA 31-JAN-97 2CGP TITLE CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CYCLIC- TITLE 2 MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*TP*AP*AP*T)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*TP*TP*AP*AP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)- COMPND 7 3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN); COMPND 12 CHAIN: A 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: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562 KEYWDS COMPLEX (TRANSCRIPTION REGULATION-DNA), DNA-BINDING, CAMP-BINDING, KEYWDS 2 ACTIVATOR, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.PASSNER,T.A.STEITZ REVDAT 5 02-AUG-23 2CGP 1 REMARK REVDAT 4 24-FEB-09 2CGP 1 VERSN REVDAT 3 12-JUN-00 2CGP 3 COMPND ATOM REVDAT 2 17-APR-00 2CGP 1 DBREF HEADER REMARK COMPND REVDAT 2 2 1 JRNL REVDAT 1 04-FEB-98 2CGP 0 JRNL AUTH J.M.PASSNER,T.A.STEITZ JRNL TITL THE STRUCTURE OF A CAP-DNA COMPLEX HAVING TWO CAMP MOLECULES JRNL TITL 2 BOUND TO EACH MONOMER. JRNL REF PROC.NATL.ACAD.SCI.USA V. 94 2843 1997 JRNL REFN ISSN 0027-8424 JRNL PMID 9096308 JRNL DOI 10.1073/PNAS.94.7.2843 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.C.SCHULTZ,G.C.SHIELDS,T.A.STEITZ REMARK 1 TITL CRYSTAL STRUCTURE OF A CAP-DNA COMPLEX: THE DNA IS BENT BY REMARK 1 TITL 2 90 DEGREES REMARK 1 REF SCIENCE V. 253 1001 1991 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.3 REMARK 3 NUMBER OF REFLECTIONS : 20270 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) : 0.237 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2012 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.700 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1728 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 173 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1580 REMARK 3 NUCLEIC ACID ATOMS : 530 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 2.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : -1.36000 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) : 0.35 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) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.130 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) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.230 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.130 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.770 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NONE 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 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2CGP 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_1000177913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 115.00 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22805 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 6.30000 REMARK 200 FOR THE DATA SET : 14.0000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 41.1000 REMARK 200 FOR SHELL : 2.600 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: PDB ENTRY 1CGP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: COMPLEX WAS CRYSTALLIZED AT PH 6.0 REMARK 280 FROM 4-6% PEG, 20% ETHYLENE GLYCOL, 0.2 M NACL, 25 MM MGCL2 AND REMARK 280 2 MM AMP. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.80000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 93.60000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 93.60000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.80000 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: 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.80000 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 MET A 0 REMARK 465 VAL A 1 REMARK 465 LEU A 2 REMARK 465 GLY A 3 REMARK 465 LYS A 4 REMARK 465 PRO A 5 REMARK 465 GLN A 6 REMARK 465 THR A 7 REMARK 465 THR A 208 REMARK 465 ARG A 209 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 LYS A 26 -7.09 77.88 REMARK 500 TYR A 41 118.03 -163.25 REMARK 500 ASP A 155 10.37 -64.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMP A 621 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMP A 622 DBREF 2CGP A 0 209 UNP P0ACJ8 CRP_ECOLI 1 210 DBREF 2CGP B 503 513 PDB 2CGP 2CGP 503 513 DBREF 2CGP C 534 548 PDB 2CGP 2CGP 534 548 SEQRES 1 B 11 DG DT DC DA DC DA DT DT DA DA DT SEQRES 1 C 15 DA DT DT DA DA DT DG DT DG DA DC DA DT SEQRES 2 C 15 DA DT SEQRES 1 A 210 MET VAL LEU GLY LYS PRO GLN THR ASP PRO THR LEU GLU SEQRES 2 A 210 TRP PHE LEU SER HIS CYS HIS ILE HIS LYS TYR PRO SER SEQRES 3 A 210 LYS SER THR LEU ILE HIS GLN GLY GLU LYS ALA GLU THR SEQRES 4 A 210 LEU TYR TYR ILE VAL LYS GLY SER VAL ALA VAL LEU ILE SEQRES 5 A 210 LYS ASP GLU GLU GLY LYS GLU MET ILE LEU SER TYR LEU SEQRES 6 A 210 ASN GLN GLY ASP PHE ILE GLY GLU LEU GLY LEU PHE GLU SEQRES 7 A 210 GLU GLY GLN GLU ARG SER ALA TRP VAL ARG ALA LYS THR SEQRES 8 A 210 ALA CYS GLU VAL ALA GLU ILE SER TYR LYS LYS PHE ARG SEQRES 9 A 210 GLN LEU ILE GLN VAL ASN PRO ASP ILE LEU MET ARG LEU SEQRES 10 A 210 SER ALA GLN MET ALA ARG ARG LEU GLN VAL THR SER GLU SEQRES 11 A 210 LYS VAL GLY ASN LEU ALA PHE LEU ASP VAL THR GLY ARG SEQRES 12 A 210 ILE ALA GLN THR LEU LEU ASN LEU ALA LYS GLN PRO ASP SEQRES 13 A 210 ALA MET THR HIS PRO ASP GLY MET GLN ILE LYS ILE THR SEQRES 14 A 210 ARG GLN GLU ILE GLY GLN ILE VAL GLY CYS SER ARG GLU SEQRES 15 A 210 THR VAL GLY ARG ILE LEU LYS MET LEU GLU ASP GLN ASN SEQRES 16 A 210 LEU ILE SER ALA HIS GLY LYS THR ILE VAL VAL TYR GLY SEQRES 17 A 210 THR ARG HET CMP A 621 22 HET CMP A 622 22 HETNAM CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE HETSYN CMP CYCLIC AMP; CAMP FORMUL 4 CMP 2(C10 H12 N5 O6 P) FORMUL 6 HOH *149(H2 O) HELIX 1 1 PRO A 9 HIS A 17 1 9 HELIX 2 2 GLU A 72 GLY A 74 5 3 HELIX 3 3 TYR A 99 VAL A 108 1 10 HELIX 4 4 ASP A 111 PHE A 136 1 26 HELIX 5 5 VAL A 139 LYS A 152 1 14 HELIX 6 6 ARG A 169 VAL A 176 1 8 HELIX 7 7 ARG A 180 ASP A 192 1 13 SHEET 1 A 3 HIS A 19 TYR A 23 0 SHEET 2 A 3 CYS A 92 SER A 98 0 SHEET 3 A 3 THR A 38 LYS A 44 -1 N LYS A 44 O GLU A 93 SHEET 1 B 3 TRP A 85 ALA A 88 0 SHEET 2 B 3 VAL A 47 LYS A 52 0 SHEET 3 B 3 GLU A 58 LEU A 64 -1 N LEU A 64 O VAL A 47 SHEET 1 C 4 MET A 157 HIS A 159 0 SHEET 2 C 4 GLY A 162 LYS A 166 0 SHEET 3 C 4 THR A 202 TYR A 206 -1 N VAL A 205 O MET A 163 SHEET 4 C 4 ILE A 196 HIS A 199 -1 N HIS A 199 O THR A 202 SITE 1 AC1 16 VAL A 49 SER A 62 ILE A 70 GLY A 71 SITE 2 AC1 16 GLU A 72 LEU A 73 ARG A 82 SER A 83 SITE 3 AC1 16 ALA A 84 ARG A 123 LEU A 124 THR A 127 SITE 4 AC1 16 SER A 128 HOH A 703 HOH A 704 HOH A 756 SITE 1 AC2 11 LYS A 57 GLU A 58 ALA A 135 PHE A 136 SITE 2 AC2 11 GLN A 170 GLY A 173 GLN A 174 GLY A 177 SITE 3 AC2 11 CYS A 178 ARG A 180 HOH A 817 CRYST1 79.190 79.190 140.400 90.00 90.00 120.00 P 31 2 1 6 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 0.012628 0.007291 0.000000 0.00000 SCALE2 0.000000 0.014581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007123 0.00000