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- PDB-3szz: Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobiu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3szz | ||||||
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Title | Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Acetate | ||||||
![]() | phosphonoacetate hydrolase | ||||||
![]() | HYDROLASE / alkaline phosphatase superfamily | ||||||
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 | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 444 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3szySC ![]() 3t00C ![]() 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-ACT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3350, 0.2 M sodium chloride, 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 |
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: 2→50 Å / Num. all: 31589 / Num. obs: 31574 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.07 / Χ2: 1.035 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 27.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SZY Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.079 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154 / 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: 69.01 Å2 / Biso mean: 18.3701 Å2 / Biso min: 4.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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