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- PDB-1f0i: THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D -

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Basic information

Entry
Database: PDB / ID: 1f0i
TitleTHE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D
ComponentsPHOSPHOLIPASE D
KeywordsHYDROLASE / Phospholipase D / alpha-beta-alpha-beta-alpha structure
Function / homology
Function and homology information


phosphatidyltransferase activity / cardiolipin biosynthetic process / phospholipase D / phospholipase D activity
Similarity search - Function
Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phospholipase D / Phospholipase D
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsLeiros, I. / Secundo, F. / Zambonelli, C. / Servi, S. / Hough, E.
CitationJournal: 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
DepositionMay 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9123
Polymers53,7221
Non-polymers1902
Water12,466692
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.280, 57.420, 68.700
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOLIPASE D


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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
10.2 Mammonium acetate1reservoir
20.1 Mcitrate/phophosphate1reservoir
327.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
MLPHAREphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementResolution: 1.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 4329 5 %RANDOM
Rwork0.1303 ---
obs0.1303 86730 99.2 %-
all-86730 --
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3719 0 10 692 4421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d2.009
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d1.959

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