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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
