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- PDB-2rb5: X-ray Crystallographic Structures Show Conservation of a Trigonal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2rb5 | ||||||
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Title | X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily. | ||||||
![]() | Putative uncharacterized protein | ||||||
![]() | UNKNOWN FUNCTION / HAD-like phosphatase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lu, Z. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.9 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.8 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rarC ![]() 2ravC ![]() 2rbkC ![]() 1ymqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28889.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Gene: Bacteroides thetaiotaomicron / Plasmid: PET-3A-HPP / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-WO6 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 46.04 % |
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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 tungstate., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→50 Å / Num. all: 124944 / Num. obs: 124944 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.03→1.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.6 / Num. unique all: 9738 / Rsym value: 0.036 / % possible all: 75.3 |
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Processing
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Refinement | Method to determine structure: AB INITIO Starting model: 1YMQ Resolution: 1.03→10 Å / Num. parameters: 23581 / Num. restraintsaints: 28371 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Displacement parameters | Biso mean: 15.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.13 Å / Num. disordered residues: 16 / Occupancy sum hydrogen: 1903 / Occupancy sum non hydrogen: 2532 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.03→1.09 Å / Rfactor Rfree error: 0.007
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