+Open data
-Basic information
Entry | Database: PDB / ID: 2nn4 | ||||||
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Title | Crystal structure of Bacillus subtilis yqgQ, Pfam DUF910 | ||||||
Components | Hypothetical protein yqgQHypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Novel fold / pfam:DUF910 / 10278a / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | YqgQ-like / YqgQ-like / YqgQ-like superfamily / YqgQ-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YqgQ Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Damodharan, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structure of YqgQ protein from Bacillus subtilis, a conserved hypothetical protein. Authors: Lakshminarasimhan, D. / 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 | 2nn4.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nn4.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/2nn4 ftp://data.pdbj.org/pub/pdb/validation_reports/nn/2nn4 | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 8701.916 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqgQ / Plasmid: pSGX4 (BS) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: P54494 #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: 2.07 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.066M sodium di-hydrogen phophate, 3.385M di-potassium hydrogen phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9801 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2006 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 12344 / Num. obs: 12344 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1075 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→47.59 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 127065.32 / 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 electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1294 Å2 / ksol: 0.390188 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→47.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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