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- PDB-1kp4: CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2 -

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Basic information

Entry
Database: PDB / ID: 1kp4
TitleCALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2
Componentsphospholipase A2
KeywordsHYDROLASE / Phospholipase A2 / Prokaryote / calcium ion
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid 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 / AB INITIO / Resolution: 1.6 Å
AuthorsMatoba, Y. / Katsube, Y. / Sugiyama, M.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The crystal structure of prokaryotic phospholipase A2.
Authors: Matoba, Y. / Katsube, Y. / Sugiyama, M.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: A novel prokaryotic phospholipase A2. Characterization, gene cloning, and solution structure
Authors: Sugiyama, M. / Ohtani, K. / Izuhara, M. / Koike, T. / Suzuki, K. / Imamura, S. / Misaki, H.
History
DepositionDec 28, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6112
Polymers13,5711
Non-polymers401
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.280, 54.250, 30.650
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit of this protein is a monomer

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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) / 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MPD, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1999 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 14730 / Num. obs: 12820 / % possible obs: 73.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.37 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.41 / Num. unique all: 1325 / % possible all: 48

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Processing

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

1faz


Resolution: 1.6→5 Å / Num. parameters: 4191 / Num. restraintsaints: 3988 / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rwork0.1496 --
all0.1496 12244 -
obs-12244 76.3 %
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1047
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 1 88 1047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0208
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.6→1.7 Å
RfactorNum. reflection% reflection
Rwork0.268 --
obs-1325 47.8 %

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