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Yorodumi- PDB-2pih: Crystal structure of Protein ymcA from Bacillus subtilis, NorthEa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pih | ||||||
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Title | Crystal structure of Protein ymcA from Bacillus subtilis, NorthEast Structural Genomics target SR375 | ||||||
Components | Protein ymcA | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ymcA / regulate community development / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information Biofilm formation YmcA / : / YheA/YmcA-like / Control of competence regulator ComK, YlbF/YmcA / YheA/YmcA-like domain superfamily / Control of competence regulator ComK, YlbF/YmcA / YheA-like fold / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Seetharaman, J. / Abashidze, M. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Abashidze, M. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Protein ymcA from Bacillus subtilis. Authors: Seetharaman, J. / Abashidze, M. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / 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 | 2pih.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pih.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/2pih ftp://data.pdbj.org/pub/pdb/validation_reports/pi/2pih | 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: 17399.084 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ymcA, BSU17020 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: O31779 #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: 2.15 Å3/Da / Density % sol: 42.79 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM NH4Cl, Tris-HCl, PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 27, 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: 2.1→50 Å / Num. all: 32962 / Num. obs: 32962 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.043 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 8.4 / Num. unique all: 3282 / Rsym value: 0.118 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å
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