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Yorodumi- PDB-1tlt: Crystal Structure of a Putative Oxidoreductase (VIRULENCE FACTOR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tlt | ||||||
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Title | Crystal Structure of a Putative Oxidoreductase (VIRULENCE FACTOR mviM HOMOLOG) | ||||||
Components | PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG) | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / NYSGXRC / T1535 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Rajashankar, K.R. / Solorzano, V. / Kniewel, R. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a Putative Oxidoreductase (VIRULENCE FACTOR mviM HOMOLOG) Authors: RAJASHANKAR, K.R. / SOLORZANO, V. / KNIEWEL, R. / LIMA, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tlt.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tlt.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 1tlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/1tlt ftp://data.pdbj.org/pub/pdb/validation_reports/tl/1tlt | HTTPS FTP |
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-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 | From similarity to pdb entry 1OFG and from packing it is infered that the biological unit is a tetramer. The second part of the biological assembly can be generated by symmetry operation x,x-y-1,-z+7/6 |
-Components
#1: Protein | Mass: 35083.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MVIM, B1068 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P75931 #2: Chemical | ChemComp-SO4 / #3: 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: 3.68 Å3/Da / Density % sol: 66.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.4M Ammonium Sulfate, 0.1M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.7→30 Å / Num. all: 29879 / Num. obs: 29879 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.31 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.119 / Net I/σ(I): 25.75 | ||||||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3.47 / Num. unique all: 2894 / Rsym value: 0.506 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: Experimental electron density. Resolution: 2.7→19.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 196115.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Anomalous signal from a Ta6Br12 clusters was used to phase the structure
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.7152 Å2 / ksol: 0.299474 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 50.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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