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Yorodumi- PDB-2nxo: Crystal structure of protein SCO4506 from Streptomyces coelicolor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nxo | ||||||
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Title | Crystal structure of protein SCO4506 from Streptomyces coelicolor, Pfam DUF178 | ||||||
Components | Hypothetical protein SCO4506 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pfam / DUf178 / NYSGXRC / 10093f / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information chorismate dehydratase / hydro-lyase activity / menaquinone biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Tyagi, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a hypothetical protein SCO4506 (gene ID: Q9L0T8) from Streptomyces coelicolor to 2.04 Angstrom resolution Authors: Tyagi, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nxo.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nxo.ent.gz | 177.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nxo_validation.pdf.gz | 458.9 KB | Display | wwPDB validaton report |
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Full document | 2nxo_full_validation.pdf.gz | 481.8 KB | Display | |
Data in XML | 2nxo_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 2nxo_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxo ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxo | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32474.861 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: Q9L0T8 / Plasmid: T7 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9L0T8 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.81 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.04→50 Å / Num. all: 76032 / Num. obs: 76032 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8 | ||||||||||||||||||
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.209 / Num. unique all: 6908 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.04→30.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 81815.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The missing residues listed in Remark 465 are due to lack of density. Residues listed having missing atoms in Remark 470 were modeled as ALA due to weak or lack of electron density. ...Details: The missing residues listed in Remark 465 are due to lack of density. Residues listed having missing atoms in Remark 470 were modeled as ALA due to weak or lack of electron density. Continuous residual density in the electron density map which may be due to unidentifiable substrate was modeled with a few waters. This was present in all four monomers.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.1264 Å2 / ksol: 0.328717 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→30.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.17 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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