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Yorodumi- PDB-3c4n: Crystal structure of DR_0571 protein from Deinococcus radiodurans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4n | ||||||
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Title | Crystal structure of DR_0571 protein from Deinococcus radiodurans in complex with ADP. Northeast Structural Genomics Consortium Target DrR125 | ||||||
Components | Uncharacterized protein DR_0571 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Cunningham, K. / Owen, L.A. / Maglaqui, M. / Baran, M.C. / Acton, T.B. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Cunningham, K. / Owen, L.A. / Maglaqui, M. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of DR_0571 protein from Deinococcus radiodurans in complex with ADP. Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Cunningham, K. / Owen, L.A. / Maglaqui, M. / Baran, M.C. / Acton, T.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 | 3c4n.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4n.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4n ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4n | 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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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42422.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant) Species: Deinococcus radiodurans / Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / Gene: DR_0571 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9RWU4 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | AUTHORS STATE THAT, ACCORDING TO THE DALI SERVER, SEVERAL STRUCTURAL HOMOLOGS OF DR_0571 HAVE FAD, ...AUTHORS STATE THAT, ACCORDING TO THE DALI SERVER, SEVERAL STRUCTURAL | Sequence details | AUTHORS STATE THAT ELECTRON DENSITY UNAMBIGUOUSLY SHOWS THAT RESIDUE 397 IS SERINE NOT GLYCINE. ...AUTHORS STATE THAT ELECTRON DENSITY UNAMBIGUOU | |
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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: 2.8 Å3/Da / Density % sol: 56 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 7.5 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Precipitant cocktail: 20% PEG 20000, 100 mM Lithium chloride, 100 mM Sodium acetate, MICROBATCH UNDER OIL, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 65421 / Num. obs: 65421 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.105 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 3.64 / Rsym value: 0.191 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 497246.54 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.7762 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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