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Yorodumi- PDB-3nrl: Crystal Structure of protein RUMGNA_01417 from Ruminococcus gnavu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nrl | ||||||
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Title | Crystal Structure of protein RUMGNA_01417 from Ruminococcus gnavus, Northeast Structural Genomics Consortium Target UgR76 | ||||||
Components | uncharacterized protein RUMGNA_01417 | ||||||
Keywords | structural genomics / unknown function / beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Thrombin, subunit H - #390 / Domain of unknown function DUF5348 / Domain of unknown function (DUF5348) / Thrombin, subunit H / Beta Barrel / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Ruminococcus gnavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Seetharaman, J. / Abashidze, M. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Abashidze, M. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target UgR76 Authors: Seetharaman, J. / Abashidze, M. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nrl.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nrl.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nrl_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 3nrl_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 3nrl_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 3nrl_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/3nrl ftp://data.pdbj.org/pub/pdb/validation_reports/nr/3nrl | HTTPS FTP |
-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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2 |
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3 |
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Unit cell |
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Details | dimer |
-Components
#1: Protein | Mass: 9817.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_01417 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: A7B1J1 #2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Cacodylate Acid (pH 6.5), 18% PEG3350, and 0.2M ammonium sulfate., VAPOR DIFFUSION, ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Cacodylate Acid (pH 6.5), 18% PEG3350, and 0.2M ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 7, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 25141 / Num. obs: 24739 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.045 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1245 / Rsym value: 0.301 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→32.24 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 171398 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.744 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.32 Å2 / Biso mean: 30.113 Å2 / Biso min: 9.58 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→32.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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