+Open data
-Basic information
Entry | Database: PDB / ID: 1nl1 | |||||||||
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Title | BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION | |||||||||
Components | ProthrombinThrombin | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 1nl1.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nl1.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nl1 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nl1 | HTTPS FTP |
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-Related structure data
Related structure data | 1nl2C 2pf2S 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
#1: Protein | Mass: 16972.398 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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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Sugar | ChemComp-NAG / | ||
#4: Chemical | ChemComp-CA / #5: 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: 3.95 Å3/Da / Density % sol: 68.88 % | |||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→32 Å / Num. obs: 21658 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.6 / % possible all: 96.3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. measured all: 150545 |
Reflection shell | *PLUS % possible obs: 96.3 % / Num. unique obs: 2064 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2pf2 Resolution: 1.9→31.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 434107.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9402 Å2 / ksol: 0.360105 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2
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Refine analyze | Luzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 32 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.97 Å |