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Yorodumi- PDB-3qod: Crystal Structure of Heterocyst Differentiation Protein, HetR fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qod | ||||||
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Title | Crystal Structure of Heterocyst Differentiation Protein, HetR from Fischerella mv11 | ||||||
Components | Heterocyst differentiation protein | ||||||
Keywords | DNA BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helix-turn-helix / transcription factor / cytosol | ||||||
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 / SAD / Resolution: 3.38 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 | 3qod.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qod.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qod_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 3qod_full_validation.pdf.gz | 498.2 KB | Display | |
Data in XML | 3qod_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 3qod_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qod ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qod | HTTPS FTP |
-Related 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: 35983.867 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: 3.35 Å3/Da / Density % sol: 63.25 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 1.0 M ammonium sulphate, 0.1 M imidazole pH 8.0, 0.2 M sodium 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: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. all: 13425 / Num. obs: 13425 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 106.5 Å2 / Rsym value: 0.14 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 3.35→3.41 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 671 / Rsym value: 0.77 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.38→40.387 Å / SU ML: 0.41 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.37 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.969 Å2 / ksol: 0.352 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112.3 Å2
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Refinement step | Cycle: LAST / Resolution: 3.38→40.387 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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