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Yorodumi- PDB-2hd3: Crystal Structure of the Ethanolamine Utilization Protein EutN fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hd3 | ||||||
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Title | Crystal Structure of the Ethanolamine Utilization Protein EutN from Escherichia coli, NESG Target ER316 | ||||||
Components | Ethanolamine utilization protein eutN | ||||||
Keywords | STRUCTURAL PROTEIN / beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Forouhar, F. / Zhang, W. / Jayaraman, S. / Zhao, L. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. ...Forouhar, F. / Zhang, W. / Jayaraman, S. / Zhao, L. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2007 Title: Functional insights from structural genomics. Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hd3.cif.gz | 211.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hd3.ent.gz | 180.1 KB | Display | PDB format |
PDBx/mmJSON format | 2hd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/2hd3 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/2hd3 | HTTPS FTP |
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-Related structure data
Related structure data | 1rtyC 1sqsC 1tm0C 1zbpC 2nv4C 2oysC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11179.307 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: eutN, cchB / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P0AEJ9 #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 | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 23% PEG 20k, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→27.74 Å / Num. all: 91657 / Num. obs: 88816 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.082 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9011 / Rsym value: 0.449 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→27.74 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 363966.45 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / 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: 40.4874 Å2 / ksol: 0.301601 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→27.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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