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Yorodumi- PDB-3qfi: X-ray crystal structure of transcriptional regulator (EF0465) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qfi | ||||||
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Title | X-ray crystal structure of transcriptional regulator (EF0465) from Enterococcus faecalis, Northeast Structural Genomics Consortium Target EfR190 | ||||||
Components | Transcriptional regulator | ||||||
Keywords | TRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / alpha-beta protein / transcriptional regulator | ||||||
Function / homology | LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / Transcriptional regulator Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hun, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of transcriptional regulator (EF0465) from Enterococcus faecalis, Northeast Structural Genomics Consortium Target EfR190 Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hun, J.F. / Northeast Structural ...Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hun, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qfi.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qfi.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qfi_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 3qfi_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 3qfi_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 3qfi_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/3qfi ftp://data.pdbj.org/pub/pdb/validation_reports/qf/3qfi | HTTPS FTP |
-Related structure data
Related structure data | 3okzS 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: 33763.941 Da / Num. of mol.: 1 / Fragment: sequence database residues 42-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF0465, EF_0465 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q838I2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.2 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil method / pH: 7.5 Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT, Precipitation solution: 0.1M HEPES (pH 7.5), 40% PEG400, and 0.1M calcium acetate, microbatch under oil method, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97877 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 4, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97877 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 7395 / Num. obs: 6316 / % possible obs: 85.4 % / Observed criterion σ(F): 0.3 / Observed criterion σ(I): 0.3 / Redundancy: 4.3 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.078 / Net I/σ(I): 14.88 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 4.3 / Num. unique all: 465 / Rsym value: 0.125 / % possible all: 65.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OKZ Resolution: 2.71→19.87 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 406735.4 / 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: 19.0745 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.71→19.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Xplor file |
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