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Yorodumi- PDB-2rar: X-ray Crystallographic Structures Show Conservation of a Trigonal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rar | ||||||
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Title | X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily. | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / HAD-like phosphatase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Lu, Z. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state. Authors: Lu, Z. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rar.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rar.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 2rar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/2rar ftp://data.pdbj.org/pub/pdb/validation_reports/ra/2rar | HTTPS FTP |
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-Related structure data
Related structure data | 2ravC 2rb5C 2rbkC 1ymqS S: Starting model for refinement C: citing same article (ref.) |
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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 | Mass: 28845.115 Da / Num. of mol.: 1 / Mutation: D10A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Plasmid: PET-3A-HPP-D10A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3plysS / References: UniProt: Q8A090 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-VN4 / |
#4: 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: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15%PEG 1500, 10mM magnesium chloride and 5mM sodium orthovanadate., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 4, 2005 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 75250 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3.8 / Num. unique all: 9933 / Rsym value: 0.236 / % possible all: 78.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YMQ Resolution: 1.52→28.24 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 713498.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.5436 Å2 / ksol: 0.311927 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.52→28.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.62 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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