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Yorodumi- PDB-3t01: Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t01 | ||||||
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Title | Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoformate | ||||||
Components | phosphonoacetate hydrolase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / alkaline phosphatase superfamily / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information phosphonoacetate hydrolase activity / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Agarwal, V. / Nair, S.K. | ||||||
Citation | Journal: Chem.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t01.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t01.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 3t01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t01_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 3t01_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 3t01_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 3t01_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/3t01 ftp://data.pdbj.org/pub/pdb/validation_reports/t0/3t01 | HTTPS FTP |
-Related structure data
Related structure data | 3szySC 3szzC 3t00C 3t02C 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: 46593.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: phnA, RB0978, SM_b21538 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92UV8, nucleotide diphosphatase | ||||
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#2: Chemical | #3: Chemical | ChemComp-PPF / | #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: 2.42 Å3/Da / Density % sol: 49.26 % |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 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: 1.6→50 Å / Num. obs: 60520 / % possible obs: 99.3 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.08 / Χ2: 1.049 / Net I/σ(I): 8.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SZY Resolution: 1.6→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.329 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.091 / 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: 94.94 Å2 / Biso mean: 17.7883 Å2 / Biso min: 3.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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