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Yorodumi- PDB-4xoo: FMN complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xoo | ||||||
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Title | FMN complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycobacterium tuberculosis (C-terminal domain) | ||||||
Components | Coenzyme F420:L-glutamate ligase | ||||||
Keywords | UNKNOWN FUNCTION / NADH-oxidase fold / FMN- and F420-binding | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rehan, A.M. / Bashiri, G. / Baker, H.M. / Baker, E.N. / Squire, C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xoo.cif.gz | 304.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xoo.ent.gz | 247.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xoo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4xoo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4xoo_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 4xoo_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/4xoo ftp://data.pdbj.org/pub/pdb/validation_reports/xo/4xoo | HTTPS FTP |
-Related structure data
Related structure data | 4xomSC 4xoqC 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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Unit cell |
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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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: fbiB, Rv3262 / Production host: Escherichia coli (E. coli) References: UniProt: P9WP79, coenzyme F420-0:L-glutamate ligase, coenzyme F420-1:gamma-L-glutamate ligase #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.86 % |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 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: 2.1→48.5 Å / Num. obs: 56408 / % possible obs: 99.4 % / Redundancy: 29.8 % / CC1/2: 1 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 30.3 % / CC1/2: 0.53 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XOM Resolution: 2.1→48.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 15.336 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.193 / 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: 44.107 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→48.5 Å
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Refine LS restraints |
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