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Yorodumi- PDB-7bzg: Structure of Bacillus subtilis HxlR, wild type in complex with fo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bzg | |||||||||||||||
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Title | Structure of Bacillus subtilis HxlR, wild type in complex with formaldehyde and DNA | |||||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Transcriptional regulator / formaldehyde sensing / DNA BINDING PROTEIN-DNA complex | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Bacillus subtilis (bacteria) Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||||||||
Authors | Zhu, R. / Chen, P.R. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nat Commun / Year: 2021 Title: Genetically encoded formaldehyde sensors inspired by a protein intra-helical crosslinking reaction. Authors: Zhu, R. / Zhang, G. / Jing, M. / Han, Y. / Li, J. / Zhao, J. / Li, Y. / Chen, P.R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bzg.cif.gz | 224 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bzg.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bzg_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7bzg_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7bzg_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 7bzg_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/7bzg ftp://data.pdbj.org/pub/pdb/validation_reports/bz/7bzg | HTTPS FTP |
-Related structure data
Related structure data | 7bzdC 7bzeC 4hqeS C: citing same article (ref.) 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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2 |
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3 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 12 molecules ABEFIJCDGHKL
#1: Protein | Mass: 14405.915 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: hxlR, BSU03470 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42406 #2: DNA chain | Mass: 6133.979 Da / Num. of mol.: 6 / Source method: obtained synthetically Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
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-Non-polymers , 6 types, 198 molecules
#3: Chemical | ChemComp-FOR / #4: Chemical | ChemComp-PGE / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-PE8 / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Details
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: 3.93 Å3/Da / Density % sol: 70.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 MES pH = 6.4, 50 mM MgCl2, 25% v/v PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 42387 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2 / Num. unique obs: 2144 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HQE Resolution: 2.9→33.409 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→33.409 Å
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Refine LS restraints |
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LS refinement shell |
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