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Yorodumi- PDB-1v6t: Crystal Structure of Lactam Utilization Protein from Pyrococcus h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v6t | ||||||
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Title | Crystal Structure of Lactam Utilization Protein from Pyrococcus horikoshii Ot3 | ||||||
Components | Hypothetical UPF0271 protein PH0986 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / TIM-BARREL / Lactam Utilization Protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / carbohydrate metabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Lactam Utilization Protein from Pyrococcus horikoshii Ot3 Authors: Mizutani, H. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v6t.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v6t.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1v6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v6t_validation.pdf.gz | 425 KB | Display | wwPDB validaton report |
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Full document | 1v6t_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 1v6t_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1v6t_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/1v6t ftp://data.pdbj.org/pub/pdb/validation_reports/v6/1v6t | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer generated by the operations: 1-x,1-y,z, x,1-y,-z and 1-x,y,-z. |
-Components
#1: Protein | Mass: 28469.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODON PLUS(DE3)-RIL / References: UniProt: O58714 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.2 Details: sodium chloride, acetate, pH 4.2, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.00, 0.97914, 0.97964 | ||||||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 18, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→30 Å / Num. all: 28634 / Num. obs: 28634 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.04 / Net I/σ(I): 20.1 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.14 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 6.35 / Num. unique all: 2822 / Rsym value: 0.232 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→28.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1854240.53 / 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: 46.696 Å2 / ksol: 0.364966 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→28.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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