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Open data
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Basic information
Entry | Database: PDB / ID: 1kp4 | ||||||
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Title | CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2 | ||||||
![]() | phospholipase A2 | ||||||
![]() | HYDROLASE / Phospholipase A2 / Prokaryote / calcium ion | ||||||
Function / homology | ![]() phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Matoba, Y. / Katsube, Y. / Sugiyama, M. | ||||||
![]() | ![]() Title: The crystal structure of prokaryotic phospholipase A2. Authors: Matoba, Y. / Katsube, Y. / Sugiyama, M. #1: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39 KB | Display | ![]() |
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PDB format | ![]() | 25.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 362.1 KB | Display | ![]() |
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Full document | ![]() | 362.6 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fazSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological unit of this protein is a monomer |
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Components
#1: Protein | Mass: 13570.782 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9Z4W2, UniProt: Q6UV28*PLUS, phospholipase A2 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 47.53 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: MPD, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1999 / Details: mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 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
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Refine analyze | Luzzati 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 step | Cycle: LAST / Resolution: 1.6→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å
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