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Yorodumi- PDB-3pe5: Three-dimensional Structure of protein A7VV38_9CLOT from Clostrid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pe5 | ||||||
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Title | Three-dimensional Structure of protein A7VV38_9CLOT from Clostridium leptum DSM 753, Northeast Structural Genomics Consortium Target QlR103 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / membrane => GO:0016020 / 3-Layer(aba) Sandwich / Alpha Beta / Cell envelope-like function transcriptional attenuator common domain protein Function and homology information | ||||||
Biological species | Clostridium leptum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.381 Å | ||||||
Authors | Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / 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: Northeast Structural Genomics Consortium Target QlR103 Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / 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 | 3pe5.cif.gz | 224.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pe5.ent.gz | 190.2 KB | Display | PDB format |
PDBx/mmJSON format | 3pe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pe5_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 3pe5_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 3pe5_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 3pe5_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/3pe5 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/3pe5 | 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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2 |
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Unit cell |
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Details | monomer,40.22 kD,95.6% |
-Components
#1: Protein | Mass: 44876.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium leptum (bacteria) / Strain: DSM 753 / Gene: CLOLEP_02443 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: A7VV38 #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: 1.98 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:0.1M MgCl2, 0.1M MES, PEG 4000 20% /w/v), microbatch under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97903 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 52123 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.6 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.381→35.397 Å / FOM work R set: 0.726 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.344 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.72 Å2 / Biso mean: 51.36 Å2 / Biso min: 14.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.381→35.397 Å
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Refinement TLS params. | Method: refined / Origin x: -22.1897 Å / Origin y: 35.9299 Å / Origin z: 75.5461 Å
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Refinement TLS group | Selection details: all |