+Open data
-Basic information
Entry | Database: PDB / ID: 6amk | ||||||
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Title | Structure of Streptomyces venezuelae BldC-whiI opt complex | ||||||
Components |
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Keywords | dna binding protein/dna / BldC / Streptomyces / MerR-like / DNA BINDING PROTEIN / dna binding protein-dna complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces venezuelae (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 3.288 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development. Authors: Schumacher, M.A. / den Hengst, C.D. / Bush, M.J. / Le, T.B.K. / Tran, N.T. / Chandra, G. / Zeng, W. / Travis, B. / Brennan, R.G. / Buttner, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6amk.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6amk.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 6amk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/6amk ftp://data.pdbj.org/pub/pdb/validation_reports/am/6amk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8161.771 Da / Num. of mol.: 2 / Mutation: L43(MSE), L58(MSE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: AQF52_4259 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M7QSG5, UniProt: F2REK9*PLUS #2: DNA chain | | Mass: 6782.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 6735.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 5.03 Å3/Da / Density % sol: 75.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% MPD, 0.1 M sodium acetate pH 5.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.28→98.9 Å / Num. obs: 16920 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 114.68 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Rsym value: 0.116 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.28→3.46 Å / Redundancy: 9.8 % / CC1/2: 0.665 / Rpim(I) all: 0.67 / Rrim(I) all: 1.59 / Rsym value: 1.43 / % possible all: 97.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.288→98.9 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 28.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 381.62 Å2 / Biso mean: 137.36 Å2 / Biso min: 82.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.288→98.9 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 4.7044 Å / Origin y: 85.6853 Å / Origin z: 69.6832 Å
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Refinement TLS group |
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