1o3q

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

Method: X-RAY DIFFRACTION D_max: 71.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CATABOLITE GENE ACTIVATOR PROTEIN

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Homooligomer Protein × 2 DNA 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 9–208	Not recorded	5'-D(APAPAPAPAPTPGPTPGPAPT)-3' × 2 5'-D(CPTPAPGPAPTPCPAPCPAPTPTPTPTPT)-3' × 2 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.23；293 K；PEG 8000, 1,4-DIOXANE, MES, NACL, MGCL2, CAMP, pH 6.23, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 3.00 Å R-free 0.318

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1O3Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CGP CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE Deposited 1991-08-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–206（205 aa） Chain B 2–206（205 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；pH 5.00, VAPOR DIFFUSION, HANGING DROP	Resolution 3.00 Å
1G6N 2.1 ANGSTROM STRUCTURE OF CAP-CAMP Deposited 2000-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；298 K；0.1mM cAMP, 0.2M sodium chloride, 5mM Tris, O.1mM EDTA, 2mM DTT, .02% sodium azide, pH 7.5, MICRODIALYSIS, temperature 298.0K	Resolution 2.10 Å
1HW5 THE CAP/CRP VARIANT T127L/S128A Deposited 2001-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：T127L, S128A Mutation：T127L, S128A	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG 4K, isoprotanol, cAMP, HEPES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.82 Å R-free 0.300
1I5Z STRUCTURE OF CRP-CAMP AT 1.9 A Deposited 2001-03-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7.8；298 K；100mM KCl, 1mM EDTA, 50mM TRIS, 35% Glycerol, cAMP, pH 7.8, LIQUID DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.242
1I6X STRUCTURE OF A STAR MUTANT CRP-CAMP AT 2.2 A Deposited 2001-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Mutation：D53H Mutation：D53H	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7.8；298 K；100MM KCL, 1MM EDTA, 50MM TRIS, 35% GLYCEROL, 20:1 CAMP:CRP, pH 7.8, LIQUID DIFFUSION, temperature 298K	Resolution 2.20 Å R-free 0.269
1J59 CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE Deposited 2002-03-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.50 Å R-free 0.279
1LB2 Structure of the E. coli alpha C-terminal domain of RNA polymerase in complex with CAP and DNA Deposited 2002-04-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric	Chain A 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；NaCl, NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.244
1O3R PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES Deposited 2003-03-18	Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 9–208（200 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.23；293 K；PEG 8000, 1,4-DIOXANE, MES, NACL, MGCL2, CAMP, pH 6.23, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 3.00 Å R-free 0.283
1O3S PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES Deposited 2003-03-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 9–208（200 aa）	Mutation：GLU181ASP	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.23；293 K；PEG 8000, 1,4-DIOXANE, MES, NACL, MGCL2, CAMP, pH 6.23, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 3.00 Å R-free 0.308
1O3T PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES Deposited 2003-03-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 9–208（200 aa） Chain B 9–208（200 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 3350, MES, NACL, MGCL2, CACL2, CAMP, NAN3, DITHIOTHREITOL, SPERMINE, N-OCTYL-B-D-GLUCOPYRANOSIDE, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.80 Å R-free 0.303
1RUN CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE Deposited 1996-05-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.70 Å
1RUO CATABOLITE GENE ACTIVATOR PROTEIN (CAP) MUTANT/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE Deposited 1996-05-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Mutation：CHAIN A, B, E181F Mutation：CHAIN A, B, E181F	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.70 Å
1ZRC 4 Crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-ICAP38 DNA Deposited 2005-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；2mM cAMP, 0.1M MES, 0.2M NaCl, 0.05M MgCl2, 5% PEG 8000, 15% Dioxane, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.290
1ZRD 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6A;17T]ICAP38 DNA Deposited 2005-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；2mM cAMP, 0.1M MES, 0.2M NaCl, 0.05M MgCl2, 5% PEG 8000, 15% Dioxane, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.297
1ZRE 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6G;17C]ICAP38 DNA Deposited 2005-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；2mM cAMP, 0.1M MES, 0.2M NaCl, 0.05M MgCl2, 5% PEG 8000, 15% Dioxane, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.283
1ZRF 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6C;17G]ICAP38 DNA Deposited 2005-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 DIO 1,4-DIETHYLENE DIOXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；2mM cAMP, 0.1M MES, 0.2M NaCl, 0.05M MgCl2, 5% PEG 8000, 15% Dioxane, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.10 Å R-free 0.266
2CGP CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE Deposited 1997-01-31	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–210（210 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；COMPLEX WAS CRYSTALLIZED AT PH 6.0 FROM 4-6% PEG, 20% ETHYLENE GLYCOL, 0.2 M NACL, 25 MM MGCL2 AND 2 MM AMP.	Resolution 2.20 Å R-free 0.296
2GZW Crystal structure of the E.coli CRP-cAMP complex Deposited 2006-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；MG ACETATE, AMMONIUM ACETATE, PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.21 Å R-free 0.278
2GZW Crystal structure of the E.coli CRP-cAMP complex Deposited 2006-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–210（209 aa） Chain D 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；MG ACETATE, AMMONIUM ACETATE, PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.21 Å R-free 0.278
3FWE Crystal Structure of the Apo D138L CAP mutant Deposited 2009-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–217（210 aa） Chain B 8–217（210 aa）	Mutation：D138L Mutation：D138L	PRO PROLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 4000 and 200mM Proline, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.277
3IYD Three-dimensional EM structure of an intact activator-dependent transcription initiation complex Deposited 2009-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 2–210（209 aa） Chain H 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 25 mM HEPES, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.2 mM cAMP；pH 8；25 mM HEPES, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.2 mM cAMP	Resolution 19.80 Å
3KCC Crystal structure of D138L mutant of Catabolite Gene Activator Protein Deposited 2009-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：D138L Mutation：D138L	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；10% PEG4000, 7% isopropanol, 3mM cAMP, 0.1M HEPES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.66 Å R-free 0.241
3N4M E. coli RNA polymerase alpha subunit C-terminal domain in complex with CAP and DNA Deposited 2010-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric	Chain A 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 PEG DI(HYDROXYETHYL)ETHER × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293.2 K；100 mM sodium acetate (pH 4.5), 625 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K	Resolution 2.99 Å R-free 0.224
3QOP Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) Deposited 2011-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：S62F Mutation：S62F	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；15% ethanol, 100MM TRIS, 3mM CAMP, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.96 Å R-free 0.244
3RDI Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) Deposited 2011-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：S63F Mutation：S63F	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；15% ETHANOL, 100MM TRIS, 3MM CAMP, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 2.95 Å R-free 0.276
3ROU Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) Deposited 2011-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：S63F Mutation：S63F	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；15% ETHANOL, 100MM TRIS, 3MM CAMP, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.247
3RPQ Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) Deposited 2011-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：S63F Mutation：S63F	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；15% ETHANOL, 100MM TRIS, 3MM CAMP, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.61 Å R-free 0.258
3RYP Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) Deposited 2011-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；10% ETHANOL, 100MM PHOSPHATE, PH 6.8, 3MM CAMP, 5% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.234
3RYR Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) Deposited 2011-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10% ETHANOL, 100MM PHOSPHATE, PH 6.8, 3MM CAMP, 5% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.273
4BH9 A structural model of CAP mutant (T127L and S128I) in the apo state Deposited 2013-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–210（209 aa）	Mutation：T127L, S128I	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 500；Pressure 1 NMR sample composition 10% WATER/90% D2O	Resolution not provided
4BHP A structural model of CAP mutant (T127L and S128I) in cGMP-bound state Deposited 2013-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–210（209 aa）	Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 500；Pressure 1 NMR sample composition 10% WATER/90% D2O	Resolution not provided
4FT8 E. coli Catabolite Activator Protein with Cobalt and Sulfate Ligands Deposited 2012-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 SO4 SULFATE ION × 13 CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；A CAP-DNA complex was screened by hanging-drop vapor diffusion with Hampton Research Crystal Screens and pregreased VDX plates. Optimization of Crystal Screen 2 condition #25 yielded ruby-red colored crystals appearing within 3 days at 20 C in 0.01 M CoCl2.6H2O, 0.1 M MES monohydrate pH 6.5 and 2.5 M (NH4)2SO4. The crystallization process yielded crystals containing only CAP protein without DNA, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.97 Å R-free 0.230
4FT8 E. coli Catabolite Activator Protein with Cobalt and Sulfate Ligands Deposited 2012-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 SO4 SULFATE ION × 13 CO COBALT (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；A CAP-DNA complex was screened by hanging-drop vapor diffusion with Hampton Research Crystal Screens and pregreased VDX plates. Optimization of Crystal Screen 2 condition #25 yielded ruby-red colored crystals appearing within 3 days at 20 C in 0.01 M CoCl2.6H2O, 0.1 M MES monohydrate pH 6.5 and 2.5 M (NH4)2SO4. The crystallization process yielded crystals containing only CAP protein without DNA, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.97 Å R-free 0.230
4HZF structure of the wild type Catabolite gene Activator Protein Deposited 2012-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10% (w/v) polyethylene glycol 3350 and 15-20% (v/v) 2-methyl-2,4-pentanediol , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.48 Å R-free 0.242
4I01 Structure of the mutant Catabolite gen activator protein V140L Deposited 2012-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7-10% PEG 3350, 15-20% MPD, 2mM cAMP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.262
4I02 structure of the mutant Catabolite gene activator protein V140A Deposited 2012-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain E 1–210（210 aa）	Mutation：V140A Mutation：V140A	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7-10% PEG3350, 15-20% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.216
4I02 structure of the mutant Catabolite gene activator protein V140A Deposited 2012-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–210（210 aa） Chain C 1–210（210 aa）	Mutation：V140A Mutation：V140A	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7-10% PEG3350, 15-20% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.216
4I02 structure of the mutant Catabolite gene activator protein V140A Deposited 2012-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–210（210 aa） Chain F 1–210（210 aa）	Mutation：V140A Mutation：V140A	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7-10% PEG3350, 15-20% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.216
4I09 structure of the mutant Catabolite gene activator protein V132L Deposited 2012-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：V132L Mutation：V132L	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7-10% Peg3350, 15-20% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.05 Å R-free 0.256
4I0A structure of the mutant Catabolite gene activator protein V132A Deposited 2012-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：V132A Mutation：V132A	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7-10% Peg3350, 15-20% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.233
4I0B structure of the mutant Catabolite gene activator protein H160L Deposited 2012-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Mutation：H160L Mutation：H160L	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7-10% Peg3350, 15-20% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.208
4R8H The role of protein-ligand contacts in allosteric regulation of the Escherichia coli Catabolite Activator Protein Deposited 2014-09-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–210（210 aa） Chain B 1–210（210 aa）	Not recorded	SP1 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL × 4 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 3350, MPD, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.46 Å R-free 0.215
5CIZ E. coli RNA polymerase alpha subunit CTD in complex with CAP and DNA: A(5)-tract binding site for alpha CTD Deposited 2015-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric	Chain A 2–210（209 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；28% (w/v) PEG4000, 0.2 M ammonium acetate, 0.01 M sarcosine, 0.1 M sodium citrate, pH 5.6	Resolution 5.01 Å R-free 0.214

39 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CRP_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 9–208

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1o3q
Deposition date deposition_date	2003-03-18
Structure title title	PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
Keywords keywords	PROTEIN-DNA COMPLEX, CAP, CAP-DNA, CATABOLITE GENE ACTIVATOR PROTEIN, CAMP RECEPTOR PROTEIN, CRP, GENE REGULATION-DNA COMPLEX; GENE REGULATION/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.02 Å
Radius of gyration Rg (electron density) rg_electron	21.25 Å
Forward intensity I(0) i0	22772400.00
Molecular weight molecular_weight	31114.0 kDa
Excluded volume excluded_volume	36739 Å³
Envelope volume envelope_volume	45874 Å³
Hydration-shell volume shell_volume	19025 Å³
Envelope diameter envelope_diameter	73.0 Å
Shell Rg shell_rg	26.64 Å
Envelope Rg envelope_rg	21.22 Å
Shape Rg shape_rg	21.24 Å
Total Rg total_rg	21.93 Å
Total atoms total_atoms	2152
Residues n_residues	226
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.4 Å
Rg (real space) rg_real	22.05 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.2770e+07
I(0) uncertainty (real space) i0_real_error	3.1660e+05
Rg (reciprocal space) rg_reciprocal	22.05 Å
I(0) (reciprocal space) i0_reciprocal	22770000.0000
Solution quality estimate total_estimate	0.8984
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	70.3 Å
Skewness Skewness skewness	0.373
Kurtosis Kurtosis kurtosis	-0.340
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1848000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	5'-D(APAPAPAPAPTPGPTPGPAP*T)-3'
Molecular weight formula_weight	3405.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	2193

AAAAATGTGAT

Entity 2 Entity 2 polymer

Description description	5'-D(CPTPAPGPAPTPCPAPCPAPTPTPTPTP*T)-3'
Molecular weight formula_weight	4534.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CTAGATCACATTTTT

Entity 3 Entity 3 polymer

Description description	CATABOLITE GENE ACTIVATOR PROTEIN
Molecular weight formula_weight	22558.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

DPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Molecular weight formula_weight	329.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1o3qa1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.4 — CAP C-terminal domain-like

Domain ID domain_id	d1o3qa2
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.3 — cAMP-binding domain-like
Family Family family	b.82.3.2 — cAMP-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	1o3qA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1o3qA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (2)

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Unit-cell length a length_a	77.150 Å
Unit-cell length b length_b	77.150 Å
Unit-cell length c length_c	143.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2521
R_work r_work	0.2520
R_free r_free	0.3180

fit	/app/data/saxs_computation/o3/1o3q/1o3q.fit
pddf	/app/data/pr_computation/o3/1o3q/1o3q.pr.out
profile	/app/data/saxs_computation/o3/1o3q/1o3q.dat

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

1. Protein Identity and Related Structures Protein Identity & Related Structures

CATABOLITE GENE ACTIVATOR PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)