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- PDB-1o3r: PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL S... -

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Basic information

Entry
Database: PDB / ID: 1o3r
TitlePROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
Components
  • 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'
  • 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3'
  • CATABOLITE GENE ACTIVATOR PROTEIN
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / CAP / CAP-DNA / CATABOLITE GENE ACTIVATOR PROTEIN / CAMP RECEPTOR PROTEIN / CRP / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription ...carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
: / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...: / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / DNA / DNA (> 10) / DNA-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsChen, S. / Vojtechovsky, J. / Parkinson, G.N. / Ebright, R.H. / Berman, H.M.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking
Authors: Chen, S. / Vojtechovsky, J. / Parkinson, G.N. / Ebright, R.H. / Berman, H.M.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Alteration of DNA Binding Specificity Through Alteration of DNA Kinking
Authors: Chen, S. / Gunasekera, A. / Zhang, X. / Kunkel, T.A. / Ebright, R.H. / Berman, H.M.
History
DepositionMar 18, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionApr 8, 2003ID: 1DB8
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'
C: 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3'
A: CATABOLITE GENE ACTIVATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1575
Polymers30,4983
Non-polymers6582
Water97354
1
B: 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'
C: 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3'
A: CATABOLITE GENE ACTIVATOR PROTEIN
hetero molecules

B: 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'
C: 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3'
A: CATABOLITE GENE ACTIVATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31310
Polymers60,9976
Non-polymers1,3174
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)76.900, 76.900, 143.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: DNA chain 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'


Mass: 3390.262 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3'


Mass: 4549.969 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein CATABOLITE GENE ACTIVATOR PROTEIN / CAP / CAMP RECEPTOR PROTEIN / CAMP-REGULATORY PROTEIN


Mass: 22558.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACJ8
#4: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.23
Details: PEG 8000, 1,4-DIOXANE, MES, NACL, MGCL2, CAMP, pH 6.23, VAPOR DIFFUSION, HANGING DROP at 293K
Components of the solutions
IDNameCrystal-IDSol-ID
11,4-DIOXANE11
2MES11
3NACL11
4MGCL211
5CAMP11
6PEG 800011
7PEG 800012
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1-0.2 mMCAP1drop
20.12-0.24 mMprotein1drop
32 mMcAMP1drop
4100 mMMES1droppH6.2
5200 mM1dropNaCl
650 mM1dropMgCl2
75-6 %(w/v)PEG80001drop
818-19 %(v/v)dioxane1drop

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 9519 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 32.75 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.8
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.306 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 9769 / Num. measured all: 94538

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS0.5refinement
CCP4(SCALA)data scaling
RefinementResolution: 3→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2839655.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.283 953 10 %RANDOM
Rwork0.233 ---
obs0.2331 9519 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.85 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 54.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.92 Å217.17 Å20 Å2
2--9.92 Å20 Å2
3----19.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 527 44 54 2206
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.751.5
X-RAY DIFFRACTIONc_mcangle_it4.312
X-RAY DIFFRACTIONc_scbond_it4.092
X-RAY DIFFRACTIONc_scangle_it5.932.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 144 8.9 %
Rwork0.247 1480 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3CMP.PARAMCMP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0104
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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