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Yorodumi- PDB-7doa: Crystal structure of Catabolite repressor acivator from E. coli i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7doa | ||||||
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Title | Crystal structure of Catabolite repressor acivator from E. coli in complex with HEPES | ||||||
Components | Catabolite repressor/activator | ||||||
Keywords | GENE REGULATION / Cra / HEPES / DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information response to fructose / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli O6:K15:H31 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Neetu, N. / Katiki, M. / Kumar, P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Catabolite repressor acivator from E. coli in complex with HEPES Authors: Neetu, N. / Katiki, M. / Kumar, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7doa.cif.gz | 244.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7doa.ent.gz | 197.3 KB | Display | PDB format |
PDBx/mmJSON format | 7doa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/7doa ftp://data.pdbj.org/pub/pdb/validation_reports/do/7doa | HTTPS FTP |
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-Related structure data
Related structure data | 2iksS S: Starting model for refinement |
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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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 60 - 333 / Label seq-ID: 83 - 356
NCS oper:
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-Components
#1: Protein | Mass: 40811.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6:K15:H31 (strain 536 / UPEC) (bacteria) Strain: 536 / UPEC / Gene: ECP_0082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A454A0X5 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.79 Å3/Da / Density % sol: 31.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: HEPES, MgCl2, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40.91 Å / Num. obs: 16445 / % possible obs: 97.78 % / Redundancy: 0.08726 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.797 Å / Num. unique obs: 3740 / CC1/2: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IKS Resolution: 2.7→40.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 49.063 / SU ML: 0.446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.87 Å2 / Biso mean: 74.035 Å2 / Biso min: 41.27 Å2
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Refinement step | Cycle: final / Resolution: 2.7→40.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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