+
Open data
-
Basic information
Entry | Database: PDB / ID: 1nl1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION | |||||||||
![]() | Prothrombin![]() | |||||||||
![]() | ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, M. / Huang, G. / Furie, B. / Seaton, B. / Furie, B.C. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1nl2C ![]() 2pf2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.88 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | pH: 7.6 / Details: pH 7.6 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9402 Å2 / ksol: 0.360105 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 32 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.97 Å |