[English] 日本語
Yorodumi- PDB-1l1s: Structure of Protein of Unknown Function MTH1491 from Methanobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l1s | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Protein of Unknown Function MTH1491 from Methanobacterium thermoautotrophicum | ||||||
Components | hypothetical protein MTH1491 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Sulphur relay, DsrE/F-like / DsrE/DsrF-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta / DrsE domain-containing protein Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Christendat, D. / Saridakis, V. / Kim, Y. / Kumar, P.A. / Xu, X. / Semesi, A. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum. Authors: Christendat, D. / Saridakis, V. / Kim, Y. / Kumar, P.A. / Xu, X. / Semesi, A. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1l1s.cif.gz | 29.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1l1s.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 1l1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l1s_validation.pdf.gz | 365.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1l1s_full_validation.pdf.gz | 367 KB | Display | |
Data in XML | 1l1s_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 1l1s_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/1l1s ftp://data.pdbj.org/pub/pdb/validation_reports/l1/1l1s | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12753.667 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: ORF1491 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O27535 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.83 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30 % MPD, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||
Crystal | *PLUS Density % sol: 57.3 % | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.93927 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 14, 2001 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→27.55 Å / Num. all: 12028 / Num. obs: 12028 / % possible obs: 92.2 % / Redundancy: 12 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.064 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 11 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 7.6 / Num. unique all: 652 / Rsym value: 0.25 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 6492 / % possible obs: 98.4 % / Num. measured all: 77390 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 12.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.3→27.55 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1761771.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.2413 Å2 / ksol: 0.371473 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→27.55 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.203 |