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Yorodumi- PDB-1nl2: BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM AND LYSOPHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nl2 | |||||||||
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Title | BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM AND LYSOPHOSPHOTIDYLSERINE | |||||||||
Components | Prothrombin | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Huang, M. / Huang, G. / Furie, B. / Seaton, B. / Furie, B.C. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins. Authors: Huang, M. / Rigby, A.C. / Morelli, X. / Grant, M.A. / Huang, G. / Furie, B. / Seaton, 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 | 1nl2.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nl2.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nl2_validation.pdf.gz | 508.7 KB | Display | wwPDB validaton report |
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Full document | 1nl2_full_validation.pdf.gz | 519.7 KB | Display | |
Data in XML | 1nl2_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1nl2_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nl2 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nl2 | HTTPS FTP |
-Related structure data
Related structure data | 1nl1SC 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16857.311 Da / Num. of mol.: 1 / Fragment: FRAGMENT 1 (residues 1-156) / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 71 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | ChemComp-LPS / | #7: 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: 3.96 Å3/Da / Density % sol: 68.91 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.6 / Details: pH 7.6 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 11566 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.8 / % possible all: 93.4 |
Reflection | *PLUS Num. measured all: 112656 |
Reflection shell | *PLUS % possible obs: 93.4 % / Num. unique obs: 1127 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NL1 Resolution: 2.3→40.98 Å / Rfactor Rfree error: 0.01 / 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: 42.0849 Å2 / ksol: 0.354745 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→40.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 41 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.38 Å |