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Yorodumi- PDB-6uw5: The crystal structure of FbiA from Mycobacterium smegmatis, GDP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uw5 | ||||||||||||
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Title | The crystal structure of FbiA from Mycobacterium smegmatis, GDP and Fo bound form | ||||||||||||
Components | Phosphoenolpyruvate transferase | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Factor 420 / Phosphotransferase / Metalloenzyme | ||||||||||||
Function / homology | Function and homology information 2-phospho-L-lactate transferase / LPPG:FO 2-phospho-L-lactate transferase activity / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Grinter, R. / Gillett, D. / Cordero, P.R.F. / Greening, C. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: mSystems / Year: 2020 Title: Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F420-0 in Mycobacteria. Authors: Grinter, R. / Ney, B. / Brammananth, R. / Barlow, C.K. / Cordero, P.R.F. / Gillett, D.L. / Izore, T. / Cryle, M.J. / Harold, L.K. / Cook, G.M. / Taiaroa, G. / Williamson, D.A. / Warden, A.C. ...Authors: Grinter, R. / Ney, B. / Brammananth, R. / Barlow, C.K. / Cordero, P.R.F. / Gillett, D.L. / Izore, T. / Cryle, M.J. / Harold, L.K. / Cook, G.M. / Taiaroa, G. / Williamson, D.A. / Warden, A.C. / Oakeshott, J.G. / Taylor, M.C. / Crellin, P.K. / Jackson, C.J. / Schittenhelm, R.B. / Coppel, R.L. / Greening, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uw5.cif.gz | 266.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uw5.ent.gz | 210.2 KB | Display | PDB format |
PDBx/mmJSON format | 6uw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uw5_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
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Full document | 6uw5_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 6uw5_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 6uw5_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/6uw5 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/6uw5 | HTTPS FTP |
-Related structure data
Related structure data | 6uvxC 6uw1C 6uw3C 6uw7C 3c3dS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 34790.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: fbiA, MSMEG_1830, MSMEI_1787 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0QTG2, 2-phospho-L-lactate transferase #2: Chemical | #3: Chemical | ChemComp-FO1 / | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | 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: 2.21 Å3/Da / Density % sol: 44.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 18 % PEG6000, 0.1 M Tris, 0.2 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2019 / Details: Silicon |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.864 Å / Num. obs: 30975 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.971 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.168 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 2.204 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2644 / CC1/2: 0.175 / Rpim(I) all: 1.623 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C3D Resolution: 2.2→45.821 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.6 / 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: 93.98 Å2 / Biso mean: 41.3258 Å2 / Biso min: 22.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→45.821 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 39.0302 Å / Origin y: 14.2258 Å / Origin z: 34.4565 Å
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Refinement TLS group |
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