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- PDB-3kcc: Crystal structure of D138L mutant of Catabolite Gene Activator Protein -

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Basic information

Entry
Database: PDB / ID: 3kcc
TitleCrystal structure of D138L mutant of Catabolite Gene Activator Protein
ComponentsCatabolite gene activator
KeywordsTRANSCRIPTION / helix-turn-helix / Activator / cAMP / cAMP-binding / DNA-binding / Nucleotide-binding / Transcription regulation
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
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / 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 ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / 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-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsTao, W.B. / Gao, Z.Q. / Zhou, J.H. / Dong, Y.H. / Yu, S.N.
CitationJournal: Int.J.Biol.Macromol. / Year: 2011
Title: The 1.6A resolution structure of activated D138L mutant of catabolite gene activator protein with two cAMP bound in each monomer
Authors: Tao, W.B. / Gao, Z.Q. / Gao, Z.Y. / Zhou, J.H. / Huang, Z.X. / Dong, Y.H. / Yu, S.N.
History
DepositionOct 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: Catabolite gene activator
B: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5466
Polymers58,2292
Non-polymers1,3174
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-40 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.536, 102.222, 53.912
Angle α, β, γ (deg.)90.00, 110.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Catabolite gene activator / cAMP receptor protein / cAMP regulatory protein


Mass: 29114.480 Da / Num. of mol.: 2 / Mutation: D138L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: crp / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACJ8
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 10% PEG4000, 7% isopropanol, 3mM cAMP, 0.1M HEPES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 59849 / Num. obs: 55401 / % possible obs: 89.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 27.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5818 / Rsym value: 0.483 / % possible all: 96.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HW5

1hw5


Resolution: 1.66→39.268 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 2712 5.04 %RANDOM
Rwork0.2041 ---
obs0.206 55401 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.047 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1043 Å20 Å2-3.9638 Å2
2--3.9472 Å20 Å2
3----0.8428 Å2
Refinement stepCycle: LAST / Resolution: 1.66→39.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 88 278 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063244
X-RAY DIFFRACTIONf_angle_d1.2184415
X-RAY DIFFRACTIONf_dihedral_angle_d15.3061205
X-RAY DIFFRACTIONf_chiral_restr0.067519
X-RAY DIFFRACTIONf_plane_restr0.004537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.66-1.69020.28591280.2469267697
1.6902-1.72270.26451380.2358269699
1.7227-1.75790.31461420.2189264097
1.7579-1.79610.24061610.22182687100
1.7961-1.83790.24291450.2108263398
1.8379-1.88380.25141560.2108265799
1.8838-1.93480.27141340.2139268999
1.9348-1.99170.2531430.2143269999
1.9917-2.0560.26821350.20772705100
2.056-2.12940.21821470.2027265899
2.1294-2.21470.22021210.2067273599
2.2147-2.31550.24211530.19792686100
2.3155-2.43750.24721630.20322696100
2.4375-2.59020.26561210.20792739100
2.5902-2.79020.2151430.19962694100
2.7902-3.07090.23331480.19352716100
3.0709-3.5150.22671450.19762747100
3.515-4.42750.21821540.1598268699
4.4275-39.27910.2211350.202264895

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