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Yorodumi- PDB-1wsc: Crystal structure of ST0229, function unknown protein from Sulfol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wsc | ||||||
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Title | Crystal structure of ST0229, function unknown protein from Sulfolobus tokodaii | ||||||
Components | Hypothetical protein ST0229 | ||||||
Keywords | Structural genomics / unknown function / function unknown protein | ||||||
Function / homology | Function and homology information Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. ...Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. / Glycoprotein, Type 4 Pilin / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å | ||||||
Authors | Murayama, T. / Tanaka, Y. / Sasaki, T. / Yasutake, Y. / Yao, M. / Tsumoto, K. / Tanaka, I. / Kumagai, I. | ||||||
Citation | Journal: To be Published Title: Crystal structure of ST0229, function unknown protein from Sulfolobus tokodaii Authors: Murayama, T. / Tanaka, Y. / Sasaki, T. / Yasutake, Y. / Yao, M. / Tsumoto, K. / Tanaka, I. / Kumagai, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wsc.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wsc.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wsc_validation.pdf.gz | 373.4 KB | Display | wwPDB validaton report |
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Full document | 1wsc_full_validation.pdf.gz | 386.8 KB | Display | |
Data in XML | 1wsc_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1wsc_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/1wsc ftp://data.pdbj.org/pub/pdb/validation_reports/ws/1wsc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Although two molecules are located in asymmetric unit, this protein exists as monomer in solution. |
-Components
#1: Protein | Mass: 25951.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q976G0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG4000, isopropanol, citrate, gamma-butyllactone, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9792, 0.9794, 0.9000 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.45→10 Å / Num. obs: 16391 / Biso Wilson estimate: 38 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.45→9.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2007051.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.236 Å2 / ksol: 0.394354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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