+Open data
-Basic information
Entry | Database: PDB / ID: 1q8b | ||||||
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Title | Structural Genomics, protein YJCS | ||||||
Components | Protein yjcS | ||||||
Keywords | Structural Genomics / Unknown Function / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Zhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The 1.9A crystal structure of protein YJCS from Bacillus subtilis Authors: Zhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q8b.cif.gz | 30.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q8b.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 1q8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q8b_validation.pdf.gz | 418.6 KB | Display | wwPDB validaton report |
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Full document | 1q8b_full_validation.pdf.gz | 420.8 KB | Display | |
Data in XML | 1q8b_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1q8b_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q8b ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q8b | 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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Details | This protein exists as dimer which related by the crystallographic 2-fold axis. |
-Components
#1: Protein | Mass: 12804.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: YJCS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: O31641 |
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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: 2.83 Å3/Da / Density % sol: 56.59 % |
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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, 0.9797, 0.94656 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 3, 2003 / 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: 1.9→50 Å / Num. all: 11760 / Num. obs: 10996 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 13.04 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 30.54 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.76 / Num. unique all: 1104 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→31.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 552905.79 / Data cutoff high rms absF: 552905.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.4281 Å2 / ksol: 0.400777 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→31.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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