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- PDB-1lwb: Crystal structure of prokaryotic phospholipase A2 at atomic resolution -

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Basic information

Entry
Database: PDB / ID: 1lwb
TitleCrystal structure of prokaryotic phospholipase A2 at atomic resolution
Componentsputative secreted protein
KeywordsHYDROLASE / Phospholipase A2 / atomic resolution / internal motion
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 / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMatoba, Y. / Sugiyama, M.
Citation
Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2003
Title: Atomic resolution structure of prokaryotic phospholipase A2: Analysis of internal motion and implication for a catalytic mechanism.
Authors: Matoba, Y. / Sugiyama, M.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: The crystal structure of prokaryotic phospholipase A2
Authors: Matoba, Y. / Katsube, Y. / Sugiyama, M.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: A novel prokaryotic phospholipase A2. Characterizaton, gene cloning and solution structure
Authors: Sugiyama, M. / Ohtani, K. / Izuhara, M. / Koike, T. / Suzuki, K. / Imamura, S. / Misaki, H.
History
DepositionMay 31, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative secreted protein


Theoretical massNumber of molelcules
Total (without water)13,5711
Polymers13,5711
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.340, 57.495, 31.807
Angle α, β, γ (deg.)90.00, 111.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis enzyme is a monomeric protein in solution.

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Components

#1: Protein putative secreted 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) / Plasmid: pIJ680 / Species (production host): Streptomyces lividans / Production host: Streptomyces lividans TK24 (bacteria) / Strain (production host): TK24
References: UniProt: Q9Z4W2, UniProt: Q6UV28*PLUS, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.48 Å3/Da / Density % sol: 17.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, lithium sulfate, sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 297 K / pH: 8 / Method: vapor diffusion, hanging drop / Details: Matoba, Y., (2002) J.Biol.Chem., 277, 20059.
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: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 0.71073 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71073 Å / Relative weight: 1
ReflectionResolution: 0.923→100 Å / Num. obs: 45532 / % possible obs: 67.48 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.65 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.21
Reflection shellResolution: 0.923→0.954 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 1.64 / Num. unique all: 1418 / % possible all: 22.75
Reflection shell
*PLUS
% possible obs: 22.75 % / Num. unique obs: 1418 / Mean I/σ(I) obs: 5.82

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FAZ

1faz


Resolution: 1.05→10 Å / Num. parameters: 10812 / Num. restraintsaints: 13414 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC TEMPERATURE FACTOR WAS INTRODUCED.
RfactorNum. reflection% reflectionSelection details
Rwork0.1034 ---
all0.1034 37649 --
obs0.1034 37649 82.2 %-
Rfree-3423 9.1 %RANDOM
Refine analyzeNum. disordered residues: 34 / Occupancy sum hydrogen: 844 / Occupancy sum non hydrogen: 1120.7
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 202 2054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0225
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.128
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.01
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.132
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1037 / Rfactor obs: 0.103 / Rfactor Rwork: 0.097
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.5
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg20.9
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg2.03

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