+Open data
-Basic information
Entry | Database: PDB / ID: 4y9i | ||||||
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Title | Structure of F420-H2 Dependent Reductase (FDR-A) msmeg_2027 | ||||||
Components | Mycobacterium tuberculosis paralogous family 11 | ||||||
Keywords | OXIDOREDUCTASE / F420 / quinone / reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.498 Å | ||||||
Authors | Ahmed, F.H. / Carr, P.D. / Jackson, C.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. Authors: Ahmed, F.H. / Carr, P.D. / Lee, B.M. / Afriat-Jurnou, L. / Mohamed, A.E. / Hong, N.S. / Flanagan, J. / Taylor, M.C. / Greening, C. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y9i.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y9i.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 4y9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y9i ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y9i | HTTPS FTP |
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-Related structure data
Related structure data | 4ybnC 4zkyC 5bncC 3r5zS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | Monomer confirmed by gel filtration |
-Components
#1: Protein | Mass: 13021.810 Da / Num. of mol.: 1 / Fragment: UNP Residues 27-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2027, MSMEI_1982, LJ00_10110 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QU01 |
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#2: Chemical | ChemComp-PO4 / |
#3: 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: 2.04 Å3/Da / Density % sol: 39.83 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 20% PEGMME5000, 0.05 M imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.498→26.195 Å / Num. obs: 16332 / % possible obs: 95.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.498→1.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.1 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R5Z Resolution: 1.498→26.195 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.04 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.498→26.195 Å
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Refine LS restraints |
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LS refinement shell |
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