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Yorodumi- PDB-1dpm: THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dpm | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIETHYL 4-METHYLBENZYLPHOSPHONATE | ||||||
Components | PHOSPHOTRIESTERASEAryldialkylphosphatase | ||||||
Keywords | HYDROLASE / MEMBRANE / PLASMID / ZINC | ||||||
Function / homology | Function and homology information aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Brevundimonas diminuta (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Vanhooke, J.L. / Benning, M.M. / Raushel, F.M. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate. Authors: Vanhooke, J.L. / Benning, M.M. / Raushel, F.M. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dpm.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dpm.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dpm ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dpm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35714.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Brevundimonas diminuta (bacteria) / References: UniProt: P0A434 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-EBP / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.21 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 41252 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 50 Å / Num. obs: 41365 / % possible obs: 88 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 70 % / Num. unique obs: 4130 / Rmerge(I) obs: 0.247 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→20 Å /
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.154 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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