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Yorodumi- PDB-7en7: The crystal structure of Escherichia coli MurR in complex with N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7en7 | ||||||
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Title | The crystal structure of Escherichia coli MurR in complex with N-acetylmuramic-acid-6-phosphate | ||||||
Components | HTH-type transcriptional regulator MurR | ||||||
Keywords | GENE REGULATION / regulator / N-acetylmuramic-acid-6-phosphate / sugar-binding | ||||||
Function / homology | Function and homology information N-acetylmuramic acid catabolic process / regulation of carbohydrate catabolic process / carbohydrate derivative metabolic process / carbohydrate derivative binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Zhang, Y. / Chen, W. / Ji, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Molecular basis for cell-wall recycling regulation by transcriptional repressor MurR in Escherichia coli. Authors: Zhang, Y. / Chen, W. / Wu, D. / Liu, Y. / Wu, Z. / Li, J. / Zhang, S.Y. / Ji, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7en7.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7en7.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 7en7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7en7_validation.pdf.gz | 747.8 KB | Display | wwPDB validaton report |
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Full document | 7en7_full_validation.pdf.gz | 747.8 KB | Display | |
Data in XML | 7en7_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 7en7_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/7en7 ftp://data.pdbj.org/pub/pdb/validation_reports/en/7en7 | HTTPS FTP |
-Related structure data
Related structure data | 7en5C 7en6C 4ivnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21356.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: murR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P77245 |
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#2: Chemical | ChemComp-J79 / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.62 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane pH 8.8, 16% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→50 Å / Num. obs: 58134 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.22→1.26 Å / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2 / Num. unique obs: 5733 / CC1/2: 0.82 / CC star: 0.949 / Rpim(I) all: 0.245 / Rrim(I) all: 0.864 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IVN Resolution: 1.22→29.206 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.53 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.43 Å2 / Biso mean: 17.6402 Å2 / Biso min: 6.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.22→29.206 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -8.355 Å / Origin y: -5.215 Å / Origin z: -14.262 Å
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Refinement TLS group | Selection details: ( CHAIN A AND RESID 95:191 ) |