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Yorodumi- PDB-2emq: Hypothetical Conserved Protein (GK1048) from Geobacillus Kaustophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2emq | ||||||
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Title | Hypothetical Conserved Protein (GK1048) from Geobacillus Kaustophilus | ||||||
Components | Hypothetical conserved protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / CBS DOMAINS / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | CBS-domain / CBS-domain / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta / Hypothetical conserved protein Function and homology information | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Rehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Hypothetical Conserved Protein (GK1048) from Geobacillus Kaustophilus Authors: Rehse, P.H. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2emq.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2emq.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 2emq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/2emq ftp://data.pdbj.org/pub/pdb/validation_reports/em/2emq | HTTPS FTP |
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-Related structure data
Related structure data | 1yavS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18092.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5L147 #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: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Li2SO4, 0.1 M Tris, 1M Na tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9794 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 16, 2006 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 12987 / Num. obs: 12961 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.4 % / Rmerge(I) obs: 0.088 / Χ2: 3.246 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 12.77 / Num. unique all: 1288 / Χ2: 2.671 / % possible all: 100 |
-Phasing
Phasing MR | Rfactor: 0.531 / Cor.coef. Fo:Fc: 0.43
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YAV Resolution: 2.5→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 39.661 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.914 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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Xplor file |
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