+Open data
-Basic information
Entry | Database: PDB / ID: 2h0l | ||||||
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Title | Crystal Structure of a Mutant of Rat Annexin A5 | ||||||
Components | Annexin A5 | ||||||
Keywords | BLOOD CLOTTING / CALCIUM / PHOSPHOLIPID MEMBRANE BINDING PROTEINS | ||||||
Function / homology | Function and homology information negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / negative regulation of blood coagulation / response to thyroid hormone / calcium-dependent phospholipid binding ...negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / negative regulation of blood coagulation / response to thyroid hormone / calcium-dependent phospholipid binding / phosphatidylserine binding / peptide hormone binding / intercalated disc / axon terminus / response to organic substance / cell projection / sarcolemma / synaptic vesicle membrane / Z disc / response to calcium ion / receptor tyrosine kinase binding / blood coagulation / synaptic vesicle / perikaryon / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / dendrite / calcium ion binding / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Langlois D'Estaintot, B. / Gallois, B. / Granier, T. / Tessier, B. / Brisson, A. | ||||||
Citation | Journal: To be Published Title: Identification of the Residues Involved in the Formation of Annexin V Trimers within 2D and 3D Crystals Authors: Brisson, A. / Granier, T. / Langlois D'Estaintot, B. / Gallois, B. / Tessier, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h0l.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h0l.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 2h0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/2h0l ftp://data.pdbj.org/pub/pdb/validation_reports/h0/2h0l | HTTPS FTP |
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-Related structure data
Related structure data | 1a8aS 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: 35584.848 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Anxa5 / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / References: UniProt: P14668 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, 300MM SODIUM ACETATA, 100MM TRIS, 3MM SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 2004 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→32.76 Å / Num. all: 10858 / Num. obs: 10858 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 44.2 Å2 / Rsym value: 0.11 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.59→2.74 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.346 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A8A Resolution: 2.59→32.76 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.918 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.133 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→32.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.65 Å / Total num. of bins used: 20
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