+Open data
-Basic information
Entry | Database: PDB / ID: 7x9r | ||||||
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Title | Crystal structure of the antirepressor GmaR | ||||||
Components | Glycosyl transferase family 2 | ||||||
Keywords | PROTEIN BINDING / Antirepressor | ||||||
Function / homology | Glycosyltransferase 2-like / Glycosyl transferase family 2 / TPR repeat profile. / Tetratricopeptide repeats / Nucleotide-diphospho-sugar transferases / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / transferase activity / Glycosyl transferase family 2 Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Cho, S.Y. / Na, H.W. / Oh, H.B. / Kwak, Y.M. / Song, W.S. / Park, S.C. / Yoon, S.I. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Structural basis of flagellar motility regulation by the MogR repressor and the GmaR antirepressor in Listeria monocytogenes. Authors: Cho, S.Y. / Na, H.W. / Oh, H.B. / Kwak, Y.M. / Song, W.S. / Park, S.C. / Jeon, W.J. / Cho, H. / Oh, B.C. / Park, J. / Kang, S.G. / Lee, G.S. / Yoon, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x9r.cif.gz | 231.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x9r.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 7x9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x9r_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 7x9r_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 7x9r_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 7x9r_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/7x9r ftp://data.pdbj.org/pub/pdb/validation_reports/x9/7x9r | HTTPS FTP |
-Related structure data
Related structure data | 7x9sC 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
#1: Protein | Mass: 58300.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) Gene: AF006_02785, B1O25_01135, B4X79_02990, B4Y57_05390, F3O35_02795 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A6YDN3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: sodium acetate, sodium cacodylate |
-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: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 32149 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 42.34 Å2 / CC1/2: 0.991 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1542 / CC1/2: 0.495 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→29.59 Å / SU ML: 0.3029 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4112 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 51.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→29.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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