+Open data
-Basic information
Entry | Database: PDB / ID: 2pqs | ||||||
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Title | Crystal Structure of the Bovine Lactadherin C2 Domain | ||||||
Components | LactadherinMFGE8 | ||||||
Keywords | CELL ADHESION / C2 domain / lactadherin / membrane binding | ||||||
Function / homology | Function and homology information acrosomal membrane / single fertilization / angiogenesis / cell adhesion / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Huang, M. / Furie, B.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal structure of the bovine lactadherin C2 domain, a membrane binding motif, shows similarity to the C2 domains of factor V and factor VIII. Authors: Lin, L. / Huai, Q. / Huang, M. / Furie, B. / Furie, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pqs.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pqs.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/2pqs ftp://data.pdbj.org/pub/pdb/validation_reports/pq/2pqs | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18095.232 Da / Num. of mol.: 4 / Fragment: C2 domain (Residues 270-427) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: MFGE8 / Plasmid: pPICz / Production host: Pichia pastoris (fungus) / References: UniProt: Q95114 #2: 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: 3.33 Å3/Da / Density % sol: 63.06 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 7.5 Details: 15% PEG4K, 20% glycerol, 50 mM HEPES, pH 7.5, EVAPORATION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å |
Detector | Detector: IMAGE PLATE |
Radiation | Monochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 19426 / Num. obs: 19057 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.26 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1171545.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.6315 Å2 / ksol: 0.339252 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→45.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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