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Yorodumi- PDB-2in5: Crystal Structure of the hypothetical lipoprotein YmcC from Esche... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2in5 | ||||||
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Title | Crystal Structure of the hypothetical lipoprotein YmcC from Escherichia coli (K12), Northeast Structural Genomics target ER552. | ||||||
Components | Hypothetical lipoprotein ymcC | ||||||
Keywords | LIPID BINDING PROTEIN / mostly beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Zhou, W. / Forouhar, F. / Seetharaman, J. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M.C. / Acton, T.B. ...Zhou, W. / Forouhar, F. / Seetharaman, J. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of the hypothetical lipoprotein YmcC from Escherichia coli (K12), Northeast Structural Genomics target ER552. Authors: Zhou, W. / Forouhar, F. / Seetharaman, J. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast ...Authors: Zhou, W. / Forouhar, F. / Seetharaman, J. / Chen, C.X. / Cunningham, K. / Ma, L.-C. / Janjua, H. / Xiao, R. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
History |
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Remark 999 | SEQUENCE MSE 1 is an initiating methionine and a modified residue |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2in5.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2in5.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 2in5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/2in5 ftp://data.pdbj.org/pub/pdb/validation_reports/in/2in5 | 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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Unit cell |
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-Components
#1: Protein | Mass: 24024.990 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12, MG1655 / Gene: ymcC, b0986 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P75884 #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: 3.06 Å3/Da / Density % sol: 59.85 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, 3.0M Sodium Chloride, 5mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37.5 Å / Num. all: 50618 / Num. obs: 50365 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.071 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.2 / Num. unique all: 7640 / Rsym value: 0.267 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→37.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 90111.02 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: Both CNS 1.1 and XtalView were used in the refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.7713 Å2 / ksol: 0.335325 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→37.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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