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Yorodumi- PDB-1vc1: Crystal structure of the TM1442 protein from Thermotoga maritima,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vc1 | ||||||
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Title | Crystal structure of the TM1442 protein from Thermotoga maritima, a homolog of the Bacillus subtilis general stress response anti-anti-sigma factor RsbV | ||||||
Components | Putative anti-sigma factor antagonist TM1442 | ||||||
Keywords | GENE REGULATION / ANTI-ANTI-SIGMA FACTOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lee, J.Y. / Ahn, H.J. / Ha, K.S. / Suh, S.W. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of the TM1442 protein from Thermotoga maritima, a homolog of the Bacillus subtilis general stress response anti-anti-sigma factor RsbV Authors: Lee, J.Y. / Ahn, H.J. / Ha, K.S. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vc1.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vc1.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vc1_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 1vc1_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 1vc1_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1vc1_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/1vc1 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/1vc1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12317.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1442 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1F5 #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: 1.88 Å3/Da / Density % sol: 34.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100mM sodium acetate, 100mM magnesium chloride, 18%(v/v) polyethylene glycol 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 1999 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 12862 / Num. obs: 12842 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16 Å2 |
Reflection shell | Resolution: 2→2.13 Å / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 807204.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.886 Å2 / ksol: 0.35435 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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