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Yorodumi- PDB-7esa: the complex structure of flavin transferase FmnB complexed with FAD -
+Open data
-Basic information
Entry | Database: PDB / ID: 7esa | ||||||
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Title | the complex structure of flavin transferase FmnB complexed with FAD | ||||||
Components | FAD:protein FMN transferase | ||||||
Keywords | TRANSFERASE / FMN transferase | ||||||
Function / homology | Function and homology information FAD:protein FMN transferase / transferase activity / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Listeria monocytogenes serotype 1/2a | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Zheng, Y.H. / Cheng, W. | ||||||
Citation | Journal: MedComm (2020) / Year: 2022 Title: Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes. Authors: Zheng, Y. / Yan, W. / Dou, C. / Zhou, D. / Chen, Y. / Jin, Y. / Yang, L. / Zeng, X. / Cheng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7esa.cif.gz | 155.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7esa.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 7esa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7esa_validation.pdf.gz | 952.3 KB | Display | wwPDB validaton report |
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Full document | 7esa_full_validation.pdf.gz | 954.6 KB | Display | |
Data in XML | 7esa_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7esa_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/7esa ftp://data.pdbj.org/pub/pdb/validation_reports/es/7esa | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37713.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria) Strain: 10403S / Gene: LMRG_02181 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H3GJF7, FAD:protein FMN transferase | ||||
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#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 51.93 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36.28 Å / Num. obs: 36579 / % possible obs: 99.97 % / Redundancy: 12.9 % / CC1/2: 0.971 / Rmerge(I) obs: 0.1193 / Net I/σ(I): 48.17 |
Reflection shell | Resolution: 1.8→1.864 Å / Num. unique obs: 3603 / CC1/2: 0.969 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→36.28 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 27.04 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.28 Å
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Refine LS restraints |
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