[English] 日本語
Yorodumi- PDB-5zhv: Crystal structure of the PadR-family transcriptional regulator Rv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zhv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv in complex with zinc ion | ||||||
Components | Transcriptional regulator | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | : / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / metal ion binding / Transcriptional regulator Rv3488 Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Meera, K. / Pal, R.K. / Arora, A. / Biswal, B.K. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Biochem. J. / Year: 2018 Title: Structural and functional characterization of the transcriptional regulator Rv3488 ofMycobacterium tuberculosisH37Rv. Authors: Kumari, M. / Pal, R.K. / Mishra, A.K. / Tripathi, S. / Biswal, B.K. / Srivastava, K.K. / Arora, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5zhv.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5zhv.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/5zhv ftp://data.pdbj.org/pub/pdb/validation_reports/zh/5zhv | HTTPS FTP |
---|
-Related structure data
Related structure data | 5zhcSC 5zi8C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: -5 - 96 / Label seq-ID: 1 - 102
|
-Components
#1: Protein | Mass: 12641.155 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: Rv3488 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I6X7F9 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.38 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate, 2.0 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→64.19 Å / Num. obs: 8086 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 768 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZHC Resolution: 2.4→64.19 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.944 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.673 / ESU R Free: 0.305 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.977 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→64.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|