[English] 日本語
Yorodumi- PDB-1wnh: Crystal structure of mouse Latexin (tissue carboxypeptidase inhibitor) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wnh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse Latexin (tissue carboxypeptidase inhibitor) | ||||||
Components | Latexin | ||||||
Keywords | HYDROLASE INHIBITOR / bi-cystatin fold / cis-proline | ||||||
Function / homology | Function and homology information metalloendopeptidase inhibitor activity / detection of temperature stimulus involved in sensory perception of pain / heparin binding / inflammatory response / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å | ||||||
Authors | Aagaard, A. / Listwan, P. / Cowieson, N. / Huber, T. / Ravasi, T. / Wells, C.A. / Flanagan, J.U. / Hume, D.A. / Kobe, B. / Martin, J.L. | ||||||
Citation | Journal: Structure / Year: 2005 Title: An Inflammatory Role for the Mammalian Carboxypeptidase Inhibitor Latexin: Relationship to Cystatins and the Tumor Suppressor TIG1 Authors: Aagaard, A. / Listwan, P. / Cowieson, N. / Huber, T. / Ravasi, T. / Wells, C.A. / Flanagan, J.U. / Kellie, S. / Hume, D.A. / Kobe, B. / Martin, J.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wnh.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wnh.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wnh_validation.pdf.gz | 430.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1wnh_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 1wnh_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1wnh_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/1wnh ftp://data.pdbj.org/pub/pdb/validation_reports/wn/1wnh | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The molecule in the asymmetric unit is assumed to represent the biological unit |
-Components
#1: Protein | Mass: 25838.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: LXN / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: P70202 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8M ammonium sulfate, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781, 0.9794, 0.9796, 0.9077 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2003 | |||||||||||||||
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 1.83→50 Å / Num. obs: 29633 / % possible obs: 99.7 % / Redundancy: 14 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.9 | |||||||||||||||
Reflection shell | Resolution: 1.83→1.9 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.83→46.47 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 606163.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.986 Å2 / ksol: 0.370558 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→46.47 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.83→1.94 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|