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- PDB-3h3u: Crystal structure of CRP (cAMP receptor Protein) from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 3h3u
TitleCrystal structure of CRP (cAMP receptor Protein) from Mycobacterium tuberculosis
ComponentsPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY)
KeywordsTRANSCRIPTION / Apo CRP / Allostery / Dimer / DNA-binding / Transcription regulation
Function / homology
Function and homology information


cell wall / cAMP binding / peptidoglycan-based cell wall / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / plasma membrane / cytosol
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / 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 ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / 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 / CRP-like cAMP-activated global transcriptional regulator / CRP-like cAMP-activated global transcriptional regulator
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKumar, P. / Joshi, D.C. / Akif, M. / Akhter, Y. / Hasnain, S.E. / Mande, S.C.
CitationJournal: Biophys.J. / Year: 2010
Title: Mapping conformational transitions in cyclic AMP receptor protein: crystal structure and normal-mode analysis of Mycobacterium tuberculosis apo-cAMP receptor protein
Authors: Kumar, P. / Joshi, D.C. / Akif, M. / Akhter, Y. / Hasnain, S.E. / Mande, S.C.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_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
A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY)
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1745
Polymers49,6532
Non-polymers5213
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-17 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.064, 84.618, 101.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY) / CRP / Transcriptional regulator / Crp/Fnr family


Mass: 24826.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3676 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O69644, UniProt: P9WMH3*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Lithium Sulphate, 15% Ethanol, 0.1M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 24, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→33.86 Å / Num. all: 10732 / Num. obs: 10723 / % possible obs: 99.9 % / Redundancy: 15.6 % / Biso Wilson estimate: 41.67 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 2.9→3.2 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1056

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D0S

3d0s


Resolution: 2.9→33.319 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 30.04 / Stereochemistry target values: ML
Details: Extra Density at the N-terminal of B Chain Modeled as cAMP. Our interpretation is subjective
RfactorNum. reflection% reflection
Rfree0.2966 514 4.79 %
Rwork0.223 10209 -
obs0.2265 10723 99.5 %
all-10732 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.451 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 104.46 Å2 / Biso mean: 44.556 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1-12.254 Å2-0 Å2-0 Å2
2---5.314 Å20 Å2
3----8.594 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 32 38 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043408
X-RAY DIFFRACTIONf_angle_d0.6314568
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr0.002605
X-RAY DIFFRACTIONf_dihedral_angle_d14.7061293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.19170.37241400.27642478X-RAY DIFFRACTION100
3.1917-3.6530.27411140.23062530X-RAY DIFFRACTION100
3.653-4.60050.28291220.18382559X-RAY DIFFRACTION100
4.6005-33.32130.27691380.21222642X-RAY DIFFRACTION99

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