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Yorodumi- PDB-1s6b: X-ray Crystal Structure of a Complex Formed Between Two Homologou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s6b | |||||||||
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Title | X-ray Crystal Structure of a Complex Formed Between Two Homologous Isoforms of Phospholipase A2 from Naja naja sagittifera: Principle of Molecular Association and Inactivation | |||||||||
Components | (Phospholipase A2 isoform ...) x 2 | |||||||||
Keywords | HYDROLASE / Phospholipase A2 / molecular conformation / enzyme activity | |||||||||
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 sagittifera (cobra) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Jabeen, T. / Sharma, S. / Singh, R.K. / Kaur, P. / Singh, T.P. | |||||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of a calcium-induced dimer of two isoforms of cobra phospholipase A2 at 1.6 A resolution. Authors: Jabeen, T. / Sharma, S. / Singh, N. / Singh, R.K. / Kaur, P. / Perbandt, M. / Betzel, C.h. / Srinivasan, A. / Singh, T.P. #1: Journal: To be Published Title: Crystal Structure of an Acidic Phospholipase A2 from Naja Naja Sagittifera at 1.5 A Resolution Authors: Singh, R.K. / Sharma, S. / Jabeen, T. / Kaur, P. / 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 | 1s6b.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s6b.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 1s6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6b ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6b | HTTPS FTP |
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-Related structure data
Related structure data | 1pshS 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
-Phospholipase A2 isoform ... , 2 types, 2 molecules AB
#1: Protein | Mass: 13220.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / Secretion: venom / References: UniProt: P60043, phospholipase A2 |
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#2: Protein | Mass: 13288.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / Secretion: venom / References: UniProt: P60044, phospholipase A2 |
-Non-polymers , 4 types, 360 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.3 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: calcium chloride, tris, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.802 / Wavelength: 0.91 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 11, 2001 / Details: MIRRORS | |||||||||
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→20 Å / Num. obs: 27946 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 17.9 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.043 / Net I/σ(I): 26 | |||||||||
Reflection shell | Resolution: 1.6→1.68 Å / Mean I/σ(I) obs: 3.02 / Rsym value: 0.329 / % possible all: 97.3 | |||||||||
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. measured all: 500751 / Rmerge(I) obs: 0.043 | |||||||||
Reflection shell | *PLUS % possible obs: 97.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PSH Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: USED CONJUGATE DIRECTION METHOD
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Displacement parameters | Biso mean: 30.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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