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Yorodumi- PDB-4lh9: Crystal structure of the refolded hood domain (Asp256-Gly295) of HetR -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lh9 | ||||||
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Title | Crystal structure of the refolded hood domain (Asp256-Gly295) of HetR | ||||||
Components | Heterocyst differentiation control protein | ||||||
Keywords | TRANSCRIPTION / single helix / loop packing around / heterocyst development / heterocyst patterning | ||||||
Function / homology | Function and homology information heterocyst development / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Nostoc (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.049 Å | ||||||
Authors | Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Chen, Y. / Zhou, C.Z. | ||||||
Citation | Journal: To be Published Title: Structural and biochemical analyses of Anabaena HetR reveal insights into the cyanobacterial heterocyst development and pattern formation Authors: Hu, H.X. / Jiang, Y.L. / Zhao, M.X. / Zhu, P. / Yang, X. / Ren, Y.M. / Wen, B. / Zhang, Z. / Wu, Q. / Chen, Y. / Zhang, C.C. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lh9.cif.gz | 27.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lh9.ent.gz | 19.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lh9_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 4lh9_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 4lh9_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 4lh9_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/4lh9 ftp://data.pdbj.org/pub/pdb/validation_reports/lh/4lh9 | HTTPS FTP |
-Related structure data
Related structure data | |
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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/peptide | Mass: 4719.375 Da / Num. of mol.: 1 / Fragment: C-terminal hood domain, UNP residues 256-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc (bacteria) / Strain: PCC 7120 / Gene: hetR / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: P27709, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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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: 3.25 Å3/Da / Density % sol: 62.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.15M NaAc, 0.1M Nacacodylate, 27% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.049→50 Å / Num. obs: 3962 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 49.89 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 3.3 / Num. unique all: 380 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.049→46.453 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.4049 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 56.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.217 Å2 / ksol: 0.352 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.18 Å2 / Biso mean: 87.496 Å2 / Biso min: 55.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.049→46.453 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.0487→2.12 Å / Total num. of bins used: 1
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Refinement TLS params. | Method: refined / Origin x: 15.0014 Å / Origin y: -1.2599 Å / Origin z: 3.1452 Å
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Refinement TLS group | Selection details: ALL |