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- PDB-1faz: THE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2 -

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Basic information

Entry
Database: PDB / ID: 1faz
TitleTHE CRYSTAL STRUCTURE OF PROKARYOTIC PHOSPHOLIPASE A2
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / phospholipase A2 / prokaryote / Streptomyces violaceoruber
Function / homology
Function and homology information


A2-type glycerophospholipase activity / arachidonate secretion / phospholipid metabolic process / metal ion binding
Similarity search - Function
Phospholipase A2, prokaryotic/fungal / Prokaryotic phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phospholipase A2 / Secreted protein
Similarity search - Component
Biological speciesStreptomyces violaceoruber (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsMatoba, Y. / katsube, Y. / Sugiyama, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The crystal structure of prokaryotic phospholipase A2.
Authors: Matoba, Y. / Katsube, Y. / Sugiyama, M.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,5711
Polymers13,5711
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.410, 57.750, 31.710
Angle α, β, γ (deg.)90.00, 111.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13570.782 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces violaceoruber (bacteria) / Description: SECRETED / Plasmid: PIJ680 / Production host: Streptomyces lividans (bacteria)
References: UniProt: Q9Z4W2, UniProt: Q6UV28*PLUS, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.85 Å3/Da / Density % sol: 33.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, lithium sulfate, sodium cacodylate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 297 K / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
220 mM1dropCaCl2
320 mg/mlprotein1drop
414 %(w/v)PEG60001reservoir
50.2 M1reservoirLi2SO4
60.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 16049 / Num. obs: 15558 / % possible obs: 77.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.41 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 34.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.276 / Num. unique all: 1174 / % possible all: 61.1
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 22015 / Rmerge(I) obs: 0.0741

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
RefinementResolution: 1.4→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1520 9.8 %RANDOM
Rwork0.188 ---
obs0.188 15483 79.8 %-
all-15558 --
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 0 127 1085
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_mcbond_it0.941.5
X-RAY DIFFRACTIONx_mcangle_it1.312
X-RAY DIFFRACTIONx_scbond_it2.042
X-RAY DIFFRACTIONx_scangle_it3.132.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 186 9.8 %
Rwork0.239 1711 -
obs--59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71
X-RAY DIFFRACTIONx_mcbond_it0.941.5
X-RAY DIFFRACTIONx_scbond_it2.042
X-RAY DIFFRACTIONx_mcangle_it1.312
X-RAY DIFFRACTIONx_scangle_it3.132.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.239

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