[English] 日本語

- PDB-3hmt: Crystal structure of the N-terminal fragment (28-126) of the huma... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3hmt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, trigonal crystal form | ||||||
![]() | Hepatocyte growth factor![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of p38MAPK cascade / Drug-mediated inhibition of MET activation / MET activates STAT3 / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of myelination / MET interacts with TNS proteins / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tolbert, W.D. | ||||||
![]() | ![]() Title: Structural basis for agonism and antagonism of hepatocyte growth factor. Authors: Tolbert, W.D. / Daugherty-Holtrop, J. / Gherardi, E. / Vande Woude, G. / Xu, H.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 48.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 291.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 296.3 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hmrC ![]() 3hmsC ![]() 3hn4C ![]() 1nk1S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | ![]() Mass: 11794.679 Da / Num. of mol.: 2 / Fragment: N-terminal domain: UNP residues 28-126 Source method: isolated from a genetically manipulated source Details: Expressed as a thioredoxin fusion protein / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.78 % Description: The structure factor file contains Friedel pairs |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.4 M sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 31, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.96→50 Å / Num. all: 23656 / Num. obs: 23656 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1274 / Rsym value: 0.24 / % possible all: 87.6 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1NK1 Resolution: 2→34.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 416044.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.2688 Å2 / ksol: 0.416442 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→34.56 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|