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Yorodumi- PDB-1g0z: SPECIFIC MUTATIONS IN KRAIT PLA2 LEAD TO DIMERIZATION OF PROTEIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g0z | ||||||
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Title | SPECIFIC MUTATIONS IN KRAIT PLA2 LEAD TO DIMERIZATION OF PROTEIN MOLECULES: CRYSTAL STRUCTURE OF KRAIT PLA2 AT 2.1 RESOLUTION | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | TOXIN / Phospholipase A2 / Homodimer / Bungarus caeruleus | ||||||
Function / homology | Function and homology information phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bungarus caeruleus (cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Singh, T.P. / Gourinath, S. / Sharma, S. / Singh, G. | ||||||
Citation | Journal: To be Published Title: Specific mutations in Krait PLA2 lead to dimerization of protein molecules: Crystal structure of Krait PLA2 at 2.1 resolution. Authors: Gourinath, S. / Singh, G. / Sharma, S. / Bhanumathi, S. / Betzel, C. / Paramsivam, M. / Srinivasan, A. / Singh, T.P. #1: Journal: To be Published Title: Three-dimensional structure of a novel phospholipase A2 from Indian common krait at 2.45 resolution. Authors: Singh, G. / Gourinath, S. / Sharma, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g0z.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g0z.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 1g0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/1g0z ftp://data.pdbj.org/pub/pdb/validation_reports/g0/1g0z | HTTPS FTP |
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-Related structure data
Related structure data | 1fe5S S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 12980.627 Da / Num. of mol.: 2 / Fragment: RESIDUES 28-145 / Source method: isolated from a natural source / Details: NATURAL PROTEIN-ISOFORM / Source: (natural) Bungarus caeruleus (cobra) / Secretion: VENOM / References: UniProt: Q6SLM1*PLUS, phospholipase A2 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50 mM Tris. HCl, 2.8 M NaCl, 1mM NaN3., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 22, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→14.3 Å / Num. all: 12541 / Num. obs: 12475 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.126 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 7.8 % / Rsym value: 0.24 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1FE5 Resolution: 2.18→14.26 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 48393.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.2238 Å2 / ksol: 0.43391 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.18→14.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.32 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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