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Yorodumi- PDB-3qoe: Crystal Structure of Heterocyst Differentiation Protein, HetR fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qoe | ||||||
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Title | Crystal Structure of Heterocyst Differentiation Protein, HetR from Fischerella mv11 | ||||||
Components | Heterocyst differentiation protein | ||||||
Keywords | DNA BINDING PROTEIN / MCSG / PSI Biology / Structural Genomics / Midwest Center for Structural Genomics / helix-turn-helix / transcription factor | ||||||
Function / homology | Function and homology information heterocyst development / serine-type endopeptidase activity / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Fischerella thermalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.004 Å | ||||||
Authors | Kim, Y. / Joachimiak, G. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria. Authors: Kim, Y. / Joachimiak, G. / Ye, Z. / Binkowski, T.A. / Zhang, R. / Gornicki, P. / Callahan, S.M. / Hess, W.R. / Haselkorn, R. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qoe.cif.gz | 220.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qoe.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qoe_validation.pdf.gz | 461.3 KB | Display | wwPDB validaton report |
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Full document | 3qoe_full_validation.pdf.gz | 562 KB | Display | |
Data in XML | 3qoe_validation.xml.gz | 36 KB | Display | |
Data in CIF | 3qoe_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qoe ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qoe | HTTPS FTP |
-Related structure data
Related structure data | 3qodSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35233.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fischerella thermalis (bacteria) / Strain: PCC 7521 / Gene: hetR / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q2ACK9 #2: 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: 3.45 Å3/Da / Density % sol: 64.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25 % PEG 4000, 50 mM Tris pH 7.5, 160 mM sodium formate, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2010 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 188807 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 55.52 Å2 / Rsym value: 0.157 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 905 / Rsym value: 0.709 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDBID 3QOD Resolution: 3.004→46.465 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.05 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.113 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.9 Å2
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Refinement step | Cycle: LAST / Resolution: 3.004→46.465 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: -0.9298 Å / Origin y: 30.6141 Å / Origin z: 5.588 Å
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Refinement TLS group | Selection details: all |