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- PDB-4xoo: FMN complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycob... -

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Basic information

Entry
Database: PDB / ID: 4xoo
TitleFMN complex of coenzyme F420:L-glutamate ligase (FbiB) from Mycobacterium tuberculosis (C-terminal domain)
ComponentsCoenzyme F420:L-glutamate ligase
KeywordsUNKNOWN 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
Coenzyme F420 biosynthesis protein FbiB, C-terminal / Bifunctional F420 biosynthesis protein FbiB / Coenzyme F420:L-glutamate ligase-like domain / Coenzyme F420:L-glutamate ligase / F420-0:Gamma-glutamyl ligase / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like ...Coenzyme F420 biosynthesis protein FbiB, C-terminal / Bifunctional F420 biosynthesis protein FbiB / Coenzyme F420:L-glutamate ligase-like domain / Coenzyme F420:L-glutamate ligase / F420-0:Gamma-glutamyl ligase / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Bifunctional F420 biosynthesis protein FbiB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRehan, A.M. / Bashiri, G. / Baker, H.M. / Baker, E.N. / Squire, C.J.
CitationJournal: 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
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coenzyme F420:L-glutamate ligase
B: Coenzyme F420:L-glutamate ligase
C: Coenzyme F420:L-glutamate ligase
D: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2368
Polymers89,4104
Non-polymers1,8254
Water90150
1
A: Coenzyme F420:L-glutamate ligase
B: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6184
Polymers44,7052
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-52 kcal/mol
Surface area16820 Å2
MethodPISA
2
C: Coenzyme F420:L-glutamate ligase
D: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6184
Polymers44,7052
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-48 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.135, 137.135, 101.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Coenzyme F420:L-glutamate ligase / Coenzyme F420-0:L-glutamate ligase / Coenzyme F420-1:gamma-L-glutamate ligase


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 / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350. lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.1→2.16 Å / Redundancy: 30.3 % / CC1/2: 0.53 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOM

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
RfactorNum. reflection% reflectionSelection details
Rfree0.26902 2790 4.9 %RANDOM
Rwork0.23155 ---
obs0.2334 53574 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 124 50 5987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196089
X-RAY DIFFRACTIONr_bond_other_d0.0010.025806
X-RAY DIFFRACTIONr_angle_refined_deg1.7292.0048379
X-RAY DIFFRACTIONr_angle_other_deg0.859313286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58722.788226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61515860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1421553
X-RAY DIFFRACTIONr_chiral_restr0.0870.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021258
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6422.573134
X-RAY DIFFRACTIONr_mcbond_other1.6412.5713133
X-RAY DIFFRACTIONr_mcangle_it2.3863.8473908
X-RAY DIFFRACTIONr_mcangle_other2.3863.8473909
X-RAY DIFFRACTIONr_scbond_it1.9212.8342955
X-RAY DIFFRACTIONr_scbond_other1.9122.8252950
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8314.184464
X-RAY DIFFRACTIONr_long_range_B_refined4.88423.5387086
X-RAY DIFFRACTIONr_long_range_B_other4.85123.5337084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 207 -
Rwork0.346 3866 -
obs--98.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.82050.3259-0.92161.2827-0.86312.38050.07940.08650.1292-0.04310.0801-0.1222-0.31140.2618-0.15950.0691-0.07620.0550.2293-0.1310.104957.216740.722231.8869
21.20090.6197-0.12041.3191-0.43682.15950.0535-0.2318-0.07370.14840.0302-0.2170.20030.514-0.08380.06280.0588-0.0190.2373-0.08690.095155.969126.394546.067
31.7997-0.3543-0.38340.93830.44061.77910.1440.0995-0.4145-0.05420.04290.01510.2390.1966-0.18690.08380.0272-0.07340.1238-0.06260.140540.79210.81977.5532
42.5495-0.3285-1.07411.6127-0.0451.72930.1019-0.1387-0.46150.0407-0.02520.1960.1151-0.1728-0.07670.0388-0.0482-0.04560.12640.06390.14725.888315.135220.5736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A253 - 448
2X-RAY DIFFRACTION2B248 - 448
3X-RAY DIFFRACTION3C249 - 448
4X-RAY DIFFRACTION4D251 - 448

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