+Open data
-Basic information
Entry | Database: PDB / ID: 1f0i | ||||||
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Title | THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D | ||||||
Components | PHOSPHOLIPASE D | ||||||
Keywords | HYDROLASE / Phospholipase D / alpha-beta-alpha-beta-alpha structure | ||||||
Function / homology | Function and homology information phosphatidyltransferase activity / cardiolipin biosynthetic process / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D / phospholipase D activity / catalytic activity Similarity search - Function | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å | ||||||
Authors | Leiros, I. / Secundo, F. / Zambonelli, C. / Servi, S. / Hough, E. | ||||||
Citation | Journal: Structure Fold.Des. / 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f0i.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f0i.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 1f0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/1f0i ftp://data.pdbj.org/pub/pdb/validation_reports/f0/1f0i | 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: 53722.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. (bacteria) / Strain: PMF References: UniProt: Q93HV1, UniProt: P84147*PLUS, phospholipase D | ||
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#2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.39 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 0.2 M NH4Ac, 0.1 M Citrate/Phosphate buffer, 27.5% PEG 4000, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→19.641 Å / Num. all: 86896 / Num. obs: 86896 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 11.652 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.204 / Num. unique all: 12587 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 261275 |
Reflection shell | *PLUS % possible obs: 99.2 % / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Resolution: 1.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor all: 0.13 / Rfactor obs: 0.1297 / Rfactor Rfree: 0.1823 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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