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Yorodumi- PDB-5eyr: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eyr | ||||||||||||
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Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 5 at 1.57A resolution | ||||||||||||
Components | EthR | ||||||||||||
Keywords | TRANSCRIPTION / EthR / repressor / Mycobacterium tuberculosis | ||||||||||||
Function / homology | Function and homology information monooxygenase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||||||||
Authors | Surade, S. / Blaszczyk, M. / Nikiforov, P.O. / Abell, C. / Blundell, T.L. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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Citation | Journal: Org.Biomol.Chem. / Year: 2016 Title: A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters. Authors: Nikiforov, P.O. / Surade, S. / Blaszczyk, M. / Delorme, V. / Brodin, P. / Baulard, A.R. / Blundell, T.L. / Abell, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eyr.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eyr.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 5eyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eyr_validation.pdf.gz | 635.1 KB | Display | wwPDB validaton report |
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Full document | 5eyr_full_validation.pdf.gz | 635.2 KB | Display | |
Data in XML | 5eyr_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 5eyr_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/5eyr ftp://data.pdbj.org/pub/pdb/validation_reports/ey/5eyr | HTTPS FTP |
-Related structure data
Related structure data | 5ezgC 5ezhC 5f04C 5f08C 5f0cC 5f0fC 5f0hC 5f1jC 5f27C 1t56S 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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-Components
#1: Protein | Mass: 25259.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: ethR_2, ethR, ethR_1, ABI38_03425, AC434_03675, ACQ94_17905, ACQ95_03225, ACQ96_05940, AFL40_4013, BN1213_00375, BN1303_02839, ERS024750_01557, ERS024751_00529, ERS024758_02192, ERS024764_ ...Gene: ethR_2, ethR, ethR_1, ABI38_03425, AC434_03675, ACQ94_17905, ACQ95_03225, ACQ96_05940, AFL40_4013, BN1213_00375, BN1303_02839, ERS024750_01557, ERS024751_00529, ERS024758_02192, ERS024764_01791, ERS094182_00752, ERS124362_00364, ERS124821_00273, ERS124823_00877, ERS124824_02674, ERS124825_01051, ERS124826_00657, ERS124827_01397, ERS124828_02317, ERS124829_02606, ERS124830_02614, ERS124831_02648, ERS124832_01045, IQ38_20160, IQ40_19545, IQ45_19480, IQ47_19420, IU13_19735, IU16_19625, TL06_14095 Production host: Escherichia coli (E. coli) / References: UniProt: A0A045KCS8, UniProt: P9WMC1*PLUS |
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#2: Chemical | ChemComp-5T0 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium Sulphate, glycerol, MES / PH range: 6.3 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 6, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.57→85.48 Å / Num. obs: 34875 / % possible obs: 97.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Net I/σ(I): 29.6 / Num. measured all: 463192 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T56 Resolution: 1.57→21.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9391 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.071
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Displacement parameters | Biso max: 89.45 Å2 / Biso mean: 32.48 Å2 / Biso min: 12.09 Å2
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Refine analyze | Luzzati coordinate error obs: 0.212 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→21.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.62 Å / Total num. of bins used: 17
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