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- PDB-4xoq: F420 complex of coenzyme F420:L-glutamate ligase (FbiB) from Myco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xoq | ||||||
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Title | F420 complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycobacterium tuberculosis (C-terminal domain) | ||||||
![]() | Coenzyme F420:L-glutamate ligase | ||||||
![]() | UNKNOWN FUNCTION / NADH-oxidase fold / FMN- and F420-binding | ||||||
Function / homology | ![]() dehydro coenzyme F420 reductase / oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor / coenzyme gamma-F420-2 biosynthetic process / coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase / coenzyme F420-0:L-glutamate ligase activity / coenzyme F420-1:gamma-L-glutamate ligase activity / F420-0 metabolic process / GTP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rehan, A.M. / Bashiri, G. / Baker, H.M. / Baker, E.N. / Squire, C.J. | ||||||
![]() | ![]() Title: Elongation of the Poly-gamma-glutamate Tail of F420 Requires Both Domains of the F420: gamma-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis. Authors: Bashiri, G. / Rehan, A.M. / Sreebhavan, S. / Baker, H.M. / Baker, E.N. / Squire, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.6 KB | Display | ![]() |
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PDB format | ![]() | 256.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xomSC ![]() 4xooC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22352.562 Da / Num. of mol.: 4 / Fragment: UNP residues 245-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: fbiB, Rv3262 / Production host: ![]() ![]() References: UniProt: P9WP79, coenzyme F420-0:L-glutamate ligase, coenzyme F420-1:gamma-L-glutamate ligase #2: Chemical | ChemComp-F42 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→48.3 Å / Num. obs: 60778 / % possible obs: 100 % / Redundancy: 14.6 % / CC1/2: 0.998 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 2 / CC1/2: 0.659 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XOM Resolution: 2.05→48.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.923 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.848 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→48.3 Å
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Refine LS restraints |
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