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Yorodumi- PDB-3h3u: Crystal structure of CRP (cAMP receptor Protein) from Mycobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h3u | ||||||
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Title | Crystal structure of CRP (cAMP receptor Protein) from Mycobacterium tuberculosis | ||||||
Components | PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY) | ||||||
Keywords | TRANSCRIPTION / 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 / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kumar, P. / Joshi, D.C. / Akif, M. / Akhter, Y. / Hasnain, S.E. / Mande, S.C. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h3u.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h3u.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 3h3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h3u_validation.pdf.gz | 798 KB | Display | wwPDB validaton report |
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Full document | 3h3u_full_validation.pdf.gz | 804 KB | Display | |
Data in XML | 3h3u_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3h3u_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/3h3u ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h3u | HTTPS FTP |
-Related structure data
Related structure data | 3d0sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Chemical | ChemComp-CMP / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 24, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.9→3.2 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1056 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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
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Solvent computation | Shrinkage 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 parameters | Biso max: 104.46 Å2 / Biso mean: 44.556 Å2 / Biso min: 7.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→33.319 Å
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Refine LS restraints |
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LS refinement shell |
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