+Open data
-Basic information
Entry | Database: PDB / ID: 1a3f | ||||||
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Title | PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | CARBOXYLIC ESTER HYDROLASE / PHOSPHOLIPASE / TRIMER / CALCIUM BINDING / ACTIVATOR SITE | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Naja naja (Indian cobra) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Segelke, B.W. / Nguyen, D. / Chee, R. / Xuong, H.N. / Dennis, E.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing. Authors: Segelke, B.W. / Nguyen, D. / Chee, R. / Xuong, N.H. / Dennis, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3f.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3f.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3f ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3f | HTTPS FTP |
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-Related structure data
Related structure data | 1a3dC 1pshS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | Mass: 13357.855 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Naja naja (Indian cobra) / Cellular location: VENOM SACK / References: UniProt: P15445, phospholipase A2 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.4 % | |||||||||||||||
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Crystal grow | Temperature: 295.5 K Details: UNBUFFERED 32.5% MONOMETHYL PEG 5K AND 0.17M SODIUM CITRATE AT 22.5 DEGREES C., temperature 295.5K | |||||||||||||||
Crystal | *PLUS Density % sol: 54 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→72.5 Å / Num. obs: 12166 / % possible obs: 79 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.5→2.69 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.24 / % possible all: 73 |
Reflection | *PLUS Num. obs: 9506 / % possible obs: 72.4 % / Num. measured all: 27711 / Rmerge(I) obs: 0.064 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PSH Resolution: 2.65→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: POST REFINEMENT / σ(F): 2
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Displacement parameters | Biso mean: 16.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight position: 250
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LS refinement shell | Resolution: 2.65→2.77 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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