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- PDB-3t00: Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobiu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t00 | ||||||
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Title | Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with vanadate | ||||||
![]() | phosphonoacetate hydrolase | ||||||
![]() | HYDROLASE / alkaline phosphatase superfamily / transition state mimic | ||||||
Function / homology | ![]() phosphonoacetate hydrolase activity / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agarwal, V. / Nair, S.K. | ||||||
![]() | ![]() Title: Structural and mechanistic insights into C-p bond hydrolysis by phosphonoacetate hydrolase. Authors: Agarwal, V. / Borisova, S.A. / Metcalf, W.W. / van der Donk, W.A. / Nair, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 76.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3szySC ![]() 3szzC ![]() 3t01C ![]() 3t02C 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: 46593.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-VO4 / | #4: Chemical | ChemComp-NI / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3350, 0.2 M NaCl, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 20, 2010 |
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 42647 / Num. obs: 41825 / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.053 / Χ2: 1.335 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 12.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SZY Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.57 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.47 Å2 / Biso mean: 28.9543 Å2 / Biso min: 10.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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