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- PDB-1v0v: Phospholipase D from Streptomyces sp. strain PMF soaked with the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v0v | ||||||
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Title | Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine. | ||||||
![]() | PHOSPHOLIPASE D | ||||||
![]() | HYDROLASE / PHOSPHOLIPASE D / SUBSTRATE SOAK / DIBUTYRYLPHOSPHATIDYLCHOLINE / DIC4PC | ||||||
Function / homology | ![]() cardiolipin synthase activity / cardiolipin biosynthetic process / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D activity / phospholipase D / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leiros, I. / McSweeney, S. / Hough, E. | ||||||
![]() | ![]() 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: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.9 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1v0rC ![]() 1v0sC ![]() 1v0tC ![]() 1v0uC ![]() 1v0wC ![]() 1v0yC ![]() 1f0iS C: citing same article ( S: Starting model for refinement |
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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: 54064.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-PO3 / |
#3: Water | ChemComp-HOH / |
Compound details | THIS DATASET DESCRIBES AN 8 DAY SUBSTRATE SOAK USING 2MM DIBUTYRYLPHOSPHATIDYLCHOLINE. A PHOSPHATE ...THIS DATASET DESCRIBES AN 8 DAY SUBSTRATE SOAK USING 2MM DIBUTYRYLP |
Sequence details | THIS SEQUENCE HAS NOT BEEN DEPOSITED TO UNIPROT AT THE TIME OF STRUCTURE DEPOSITION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.4 % |
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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. CRYSTALS WERE THEREAFTER BACKSOAKED TWICE IN A PHOSPHATE- FREE BUFFER TO REMOVE TRACE-AMOUNTS OF PHOSPHATE., pH 5.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→69.01 Å / Num. obs: 41858 / % possible obs: 90.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 4.9 / % possible all: 64.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: BASED ON PDB ENTRY 1F0I Resolution: 1.7→69.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.193 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.116 / 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: 17.98 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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