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Yorodumi- PDB-3lrx: Crystal Structure of the C-terminal domain (residues 78-226) of P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lrx | ||||||
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Title | Crystal Structure of the C-terminal domain (residues 78-226) of PF1911 hydrogenase from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR246A | ||||||
Components | Putative hydrogenase | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information pyrimidine nucleotide biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Belote, R.L. / Everett, J.K. / Nair, R. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Belote, R.L. / 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 PfR246A Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Belote, R.L. / 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 | 3lrx.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lrx.ent.gz | 135.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/3lrx ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lrx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | In the crystal, the protein forms a hexamer, whereas in the solution it is a dimer according to the static light scattering data. |
-Components
#1: Protein | Mass: 18184.924 Da / Num. of mol.: 6 / Fragment: sequence database residues 78-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1911 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8TZS3, ferredoxin-NADP+ reductase #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 grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 100mM Hepes (pH 7), 18% PEG3350, and 100mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 1, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 45438 / Num. obs: 43303 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.074 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4201 / Rsym value: 0.396 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→19.3 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 268568.562 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.98 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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