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Yorodumi- PDB-5ua1: Mycobacterium tuberculosis KstR in complex with a 18-bp DNA operator -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ua1 | ||||||
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Title | Mycobacterium tuberculosis KstR in complex with a 18-bp DNA operator | ||||||
Components |
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Keywords | Transcription/DNA / KstR / DNA / complex / transcriptional regulator / TetR family transcriptional repressor / Structural Genomics TB Structural Genomics Consortium / TBSGC / Transcription-DNA complex | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ho, N.A.T. / Dawes, S.S. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To Be Published Title: Crystal structure of KstR in complex with cognate DNA operator Authors: Ho, N.A.T. / Dawes, S.S. / Baker, E.N. / Lott, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ua1.cif.gz | 119.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ua1.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ua1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ua1_validation.pdf.gz | 470.7 KB | Display | wwPDB validaton report |
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Full document | 5ua1_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 5ua1_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5ua1_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/5ua1 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/5ua1 | HTTPS FTP |
-Related structure data
Related structure data | 5ua2C 5cxgS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 22352.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: kstR, Rv3574 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96856 |
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-DNA chain , 2 types, 4 molecules CEDF
#2: DNA chain | Mass: 5514.603 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria) #3: DNA chain | Mass: 5514.603 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria) |
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-Non-polymers , 3 types, 8 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 15% PEG 3350, 9% MPD, 0.2 M Li2SO4, 0.1 M imidazole-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.56 Å / Num. obs: 24284 / % possible obs: 100 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.155 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.47 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CXG Resolution: 2.9→46.853 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→46.853 Å
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Refine LS restraints |
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LS refinement shell |
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