+Open data
-Basic information
Entry | Database: PDB / ID: 4uds | ||||||
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Title | Crystal structure of MbdR regulator from Azoarcus sp. CIB | ||||||
Components | MBDR REGULATOR | ||||||
Keywords | TRANSCRIPTION / TETR FAMILY | ||||||
Function / homology | Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Orthogonal Bundle / Mainly Alpha Function and homology information | ||||||
Biological species | AZOARCUS SP. CIB (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å | ||||||
Authors | Liu, H. / Liu, H.X. / MacMahon, S.A. / Juarez, J.F. / Zamarro, M.T. / Eberlein, C. / Boll, M. / Carmona, M. / Diaz, E. / Naismith, J.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Unraveling the Specific Regulation of the Mbd Central Pathway for the Anaerobic Degradation of 3-Methylbenzoate. Authors: Juarez, J.F. / Liu, H. / Zamarro, M.T. / Mcmahon, S. / Liu, H. / Naismith, J.H. / Eberlein, C. / Boll, M. / Carmona, M. / Diaz, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uds.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uds.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uds_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 4uds_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 4uds_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4uds_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/4uds ftp://data.pdbj.org/pub/pdb/validation_reports/ud/4uds | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24240.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AZOARCUS SP. CIB (bacteria) / Production host: ESCHERICHIA COLI (E. coli) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.26 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→52.35 Å / Num. obs: 17349 / % possible obs: 95.7 % / Observed criterion σ(I): 4.1 / Redundancy: 7 % / Rmerge(I) obs: 0.07 |
-Processing
Software | Name: REFMAC / Version: 5.6.0111 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.76→52.35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.834 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→52.35 Å
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Refine LS restraints |
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