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Yorodumi- PDB-1nc5: Structure of Protein of Unknown Function of YteR from Bacillus Su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nc5 | ||||||
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Title | Structure of Protein of Unknown Function of YteR from Bacillus Subtilis | ||||||
Components | hypothetical protein yTERHypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HELIX BARREL / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information unsaturated rhamnogalacturonyl hydrolase / unsaturated rhamnogalacturonyl hydrolase activity / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Zhang, R. / Lozondra, L. / Korolev, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Authors: Zhang, R. / Minh, T. / Lezondra, L. / Korolev, S. / Moy, S.F. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nc5.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nc5.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1nc5 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1nc5 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This protein (APC1644) existed as monomer |
-Components
#1: Protein | Mass: 43021.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YTER / Plasmid: MSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: O34559 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.3 M Nacitrate, 0.1M Tris , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.94656 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 12, 2002 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→50 Å / Num. obs: 59605 / % possible obs: 99.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 20.36 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 34.88 | ||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.47 / Num. unique all: 5741 / % possible all: 98.3 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 59188 | ||||||||||||
Reflection shell | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.56 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: none Resolution: 1.6→44.49 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: In the cns refinement (hlml target), the Friedel's pair was treated as two seperated reflections.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3677 Å2 / ksol: 0.389443 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze | Luzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.15 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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