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Yorodumi- PDB-2aw6: Structure of a bacterial peptide pheromone/receptor complex and i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aw6 | ||||||
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Title | Structure of a bacterial peptide pheromone/receptor complex and its mechanism of gene regulation | ||||||
Components |
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Keywords | TRANSCRIPTION / Repressor / pheromone / DNA binding / regulatory | ||||||
Function / homology | Function and homology information transcription repressor complex / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Shi, K. / Brown, C.K. / Gu, Z.Y. / Kozlowicz, B.K. / Dunny, G.M. / Ohlendorf, D.H. / Earhart, C.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis. Authors: Shi, K. / Brown, C.K. / Gu, Z.Y. / Kozlowicz, B.K. / Dunny, G.M. / Ohlendorf, D.H. / Earhart, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aw6.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aw6.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 2aw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aw6_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 2aw6_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 2aw6_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2aw6_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/2aw6 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/2aw6 | HTTPS FTP |
-Related structure data
Related structure data | 2awiSC 2axuC 2axvC 2axzC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 1 - 286 / Label seq-ID: 1 - 286
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-Components
#1: Protein | Mass: 37137.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04114 #2: Protein/peptide | Mass: 790.001 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: 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: 2.6 Å3/Da / Density % sol: 53.2 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 Details: PEG4000, citrate-phosphate, pH 7.0, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 |
Detector | Date: Mar 2, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→47.42 Å / Num. obs: 16419 / % possible obs: 94.9 % / Observed criterion σ(F): 1.2 / Observed criterion σ(I): 1.5 / Redundancy: 5.97 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.1 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2AWI Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.294 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 3.058 / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.506 Å2
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
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Xplor file |
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