+Open data
-Basic information
Entry | Database: PDB / ID: 7ewd | ||||||
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Title | Mycobacterium tuberculosis HigA2 (Form II) | ||||||
Components | Putative antitoxin HigA2 | ||||||
Keywords | DNA BINDING PROTEIN / Antitoxin / HigA2 | ||||||
Function / homology | HigA2-like, helix-turn-helix domain / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Putative antitoxin HigA2 Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Kim, H.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Iucrj / Year: 2021 Title: Chasing the structural diversity of the transcription regulator Mycobacterium tuberculosis HigA2. Authors: Richardson, W. / Kang, G.W. / Lee, H.J. / Kwon, K.M. / Kim, S. / Kim, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ewd.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ewd.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ewd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/7ewd ftp://data.pdbj.org/pub/pdb/validation_reports/ew/7ewd | HTTPS FTP |
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-Related structure data
Related structure data | 7ewcSC 7eweC 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
#1: Protein | Mass: 11309.927 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: higA2, Rv2021c, RVBD_2021c, LH57_11010, P425_02092 / Production host: Escherichia coli (E. coli) / References: UniProt: O53467 |
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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: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% (w/v) PEK 8000, 8% (v/v) ethylene glycol, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. obs: 7877 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.979 / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 3.2→3.26 Å / Num. unique obs: 382 / CC1/2: 0.892 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ewc Resolution: 3.2→38.96 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 18.131 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 260.31 Å2 / Biso mean: 99.6 Å2 / Biso min: 41.33 Å2
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Refinement step | Cycle: final / Resolution: 3.2→38.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.28 Å / Rfactor Rfree error: 0
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