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Yorodumi- PDB-7kl8: Structure of F420 binding protein Rv1558 from Mycobacterium tuber... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kl8 | ||||||
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Title | Structure of F420 binding protein Rv1558 from Mycobacterium tuberculosis with F420 bound | ||||||
Components | Deazaflavin-dependent nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / F420 / FDOR | ||||||
Function / homology | Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors / F420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / FMN-binding split barrel / Oxidoreductases / oxidoreductase activity / COENZYME F420-3 / COENZYME F420 / Deazaflavin-dependent nitroreductase Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.469 Å | ||||||
Authors | Lee, B.M. / Tan, L.L. / Jackson, C.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Potency boost of a Mycobacterium tuberculosis dihydrofolate reductase inhibitor by multienzyme F 420 H 2 -dependent reduction. Authors: Aragaw, W.W. / Lee, B.M. / Yang, X. / Zimmerman, M.D. / Gengenbacher, M. / Dartois, V. / Chui, W.K. / Jackson, C.J. / Dick, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kl8.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kl8.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 7kl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kl8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7kl8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7kl8_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7kl8_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/7kl8 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/7kl8 | HTTPS FTP |
-Related structure data
Related structure data | 3r5rS 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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Unit cell |
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-Components
#1: Protein | Mass: 15695.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: CAB90_01754, DSI38_14865, E5M52_02625, ERS007663_00055, ERS007665_00099, ERS007670_00350, ERS007679_03028, ERS007681_00165, ERS007688_03909, ERS007703_00001, ERS007720_01803, ERS007722_00045, ...Gene: CAB90_01754, DSI38_14865, E5M52_02625, ERS007663_00055, ERS007665_00099, ERS007670_00350, ERS007679_03028, ERS007681_00165, ERS007688_03909, ERS007703_00001, ERS007720_01803, ERS007722_00045, ERS007741_00109, ERS013471_00965, ERS023446_01350, ERS024276_03277, ERS027646_02383, ERS027659_01827, ERS027661_02140, ERS075361_00097, ERS094182_01470, F6W99_00117, FRD82_03855, SAMEA2683035_03185 Production host: Escherichia coli (E. coli) References: UniProt: A0A045KKP3, Oxidoreductases, Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors #2: Chemical | ChemComp-6J4 / | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-F42 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 6.47 Å3/Da / Density % sol: 80.99 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium citrate pH 5.8, 0.5 M Ammonium sulfate, 1 M Lithium sulfate, and 3 % Glycerol (v/v) |
-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: 0.953719973564 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953719973564 Å / Relative weight: 1 |
Reflection | Resolution: 2.469→48.99 Å / Num. obs: 30473 / % possible obs: 99.7 % / Redundancy: 78.5 % / CC1/2: 1 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.028 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.469→2.558 Å / Rmerge(I) obs: 5.963 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2899 / CC1/2: 0.416 / Rpim(I) all: 0.945 / % possible all: 97.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R5R Resolution: 2.469→48.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.957 / SU B: 14.276 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.469→48.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.469→2.531 Å
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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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