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Yorodumi- PDB-2rb6: X-Ray structure of the protein Q8EI81. Northeast Structural Genom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rb6 | ||||||
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Title | X-Ray structure of the protein Q8EI81. Northeast Structural Genomics Consortium target SoR78A | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / Q8EI81_SHEON / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Protein of unknown function DUF903 / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta / plasma membrane / Uncharacterized protein Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-Ray structure of the protein Q8EI81. Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rb6.cif.gz | 32.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rb6.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 2rb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/2rb6 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/2rb6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
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: 7512.694 Da / Num. of mol.: 2 / Fragment: Residues 25-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_0963 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EI81 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 6 Details: 0.1M NaNO3, 0.1M MES, 20% PEG 4000, pH 6.0, MICROBATCH UNDER OIL, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 14617 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 50.5 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 5.3 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→19.92 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 129958.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing. Bulk solvent model was used in refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.8393 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 41.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
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Xplor file |
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