[English] 日本語
Yorodumi- PDB-1rcu: X-RAY STRUCTURE OF TM1055 NORTHEAST STRUCTURAL GENOMICS CONSORTIU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rcu | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY STRUCTURE OF TM1055 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET VT76 | ||||||
Components | conserved hypothetical protein VT76 | ||||||
Keywords | Structural Genomics / unknown function / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Conserved hypothetical protein CHP00725 / SLOG cluster4 / SLOG cluster4 family / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / cytosol / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Kuzin, A.P. / Chen, Y. / Edwards, A. / Skarina, T. / Savchenko, A. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: X-RAY STRUCTURE OF TM1055 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET VT76 Authors: Kuzin, A.P. / Edwards, A. / Skarina, T. / Savchenko, A. / Tong, L. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rcu.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rcu.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rcu_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rcu_full_validation.pdf.gz | 478.4 KB | Display | |
Data in XML | 1rcu_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 1rcu_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/1rcu ftp://data.pdbj.org/pub/pdb/validation_reports/rc/1rcu | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21355.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* / References: UniProt: Q9X0E5 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.95 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M sodium Formate, 0.05M Tris, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97879, 0.97907, 0.98027 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 43759 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.096 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.5→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 194540.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.1654 Å2 / ksol: 0.341112 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.97 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||
Xplor file |
|