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Yorodumi- PDB-1u8s: Crystal structure of putative glycine cleavage system transcripti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u8s | ||||||
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Title | Crystal structure of putative glycine cleavage system transcriptional repressor | ||||||
Components | glycine cleavage system transcriptional repressor, putative | ||||||
Keywords | TRANSCRIPTION / Structural Genomics / Protein Structure Initiative (PSI) / Domain Swapping / ACT Domain / Glycine Cleavage System | ||||||
Function / homology | Function and homology information DNA-templated transcription / regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | ||||||
Authors | Kumaran, D. / Swaminathan, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative glycine cleavage system transcriptional repressor Authors: Kumaran, D. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u8s.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u8s.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1u8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u8s_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 1u8s_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 1u8s_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1u8s_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/1u8s ftp://data.pdbj.org/pub/pdb/validation_reports/u8/1u8s | 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: 21393.232 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KQ45 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.45→50 Å / Num. all: 14865 / Num. obs: 14865 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.5 | |||||||||||||||
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.34 / Num. unique all: 1451 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues 131-138 (Chain A), 132-138 (B chain) and 181-182 (both chains) were not visible in the electron density map.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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