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Yorodumi- PDB-3e0h: Crystal structure of an uncharacterized protein from Chlorobium t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e0h | ||||||
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Title | Crystal structure of an uncharacterized protein from Chlorobium tepidum. NorthEast Structural Genomics target CtR107. | ||||||
Components | uncharacterized protein | ||||||
Keywords | structural genomics / unknown function / uncharacterized protein / Chlorobium tepidum / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Chlorobaculum tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å | ||||||
Authors | Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized protein from Chlorobium tepidum. NorthEast Structural Genomics target CtR107. Authors: Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / 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 | 3e0h.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e0h.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e0h_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 3e0h_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 3e0h_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3e0h_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/3e0h ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e0h | 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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Unit cell |
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-Components
#1: Protein | Mass: 17329.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KFZ1 |
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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: 1.93 Å3/Da / Density % sol: 36.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1 Details: Sodium bromide 0.1M,MES 0.1M, PEG 20000 40%, pH 4.1, VAPOR DIFFUSION, SITTING DROP, 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: Jul 7, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 23778 / Num. obs: 23778 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.09 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 10.2 / Num. unique all: 2380 / Rsym value: 0.318 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.81→37.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 175976.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.5088 Å2 / ksol: 0.415555 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→37.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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