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Yorodumi- PDB-1v0r: Tungstate-inhibited phospholipase D from Streptomyces sp. strain PMF -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v0r | ||||||
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Title | Tungstate-inhibited phospholipase D from Streptomyces sp. strain PMF | ||||||
Components | PHOSPHOLIPASE D | ||||||
Keywords | HYDROLASE / PHOSPHOLIPASE D / TUNGSTATE-INHIBITED | ||||||
Function / homology | Function and homology information phosphatidyltransferase activity / cardiolipin biosynthetic process / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D / phospholipase D activity Similarity search - Function | ||||||
Biological species | STREPTOMYCES SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Leiros, I. / McSweeney, S. / Hough, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The Reaction Mechanism of Phospholipase D from Streptomyces Sp. Strain Pmf. Snapshots Along the Reaction Pathway Reveal a Pentacoordinate Reaction Intermediate and an Unexpected Final Product Authors: Leiros, I. / Mcsweeney, S. / Hough, E. #1: Journal: Structure / Year: 2000 Title: The First Crystal Structure of a Phospholipase D Authors: Leiros, I. / Secundo, F. / Zambonelli, C. / Servi, S. / Hough, E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v0r.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v0r.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 1v0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/1v0r ftp://data.pdbj.org/pub/pdb/validation_reports/v0/1v0r | HTTPS FTP |
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-Related structure data
Related structure data | 1v0sC 1v0tC 1v0uC 1v0vC 1v0wC 1v0yC 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: 54064.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES SP. (bacteria) / Strain: PMF / References: UniProt: P84147*PLUS, phospholipase D |
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#2: Chemical | ChemComp-WO5 / |
#3: Water | ChemComp-HOH / |
Sequence details | THIS SEQUENCE HAS NOT BEEN DEPOSITED TO UNIPROT AT THE TIME OF STRUCTURE DEPOSITION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.4 % Description: THIS IS THE REMOTE WAVELENGTH OF A MAD DATA SET. |
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Crystal grow | pH: 5.4 Details: 0.2 M NH4AC, 0.1 M CITRATE PHOSPHATE BUFFER AT PH5.4, 27.5% PEG 4000, pH 5.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.886 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→69.01 Å / Num. obs: 46471 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→69.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.02 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS THAT HAVE BEEN MODELED WITH AN OCCUPANCY OF 0.00.
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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 mean: 18.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→69.01 Å
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Refine LS restraints |
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