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- PDB-4xoq: F420 complex of coenzyme F420:L-glutamate ligase (FbiB) from Myco... -

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Basic information

Entry
Database: PDB / ID: 4xoq
TitleF420 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
COENZYME F420 / Bifunctional F420 biosynthesis protein FbiB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)92,79311
Polymers89,4104
Non-polymers3,3837
Water7,170398
1
A: Coenzyme F420:L-glutamate ligase
B: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4446
Polymers44,7052
Non-polymers1,7394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-76 kcal/mol
Surface area17140 Å2
MethodPISA
2
C: Coenzyme F420:L-glutamate ligase
D: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3485
Polymers44,7052
Non-polymers1,6433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-60 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.612, 136.612, 101.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-613-

HOH

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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-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H36N5O18P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
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: Nov 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 3026 5 %RANDOM
Rwork0.21158 ---
obs0.21328 57682 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.848 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.05→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5905 0 132 398 6435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196184
X-RAY DIFFRACTIONr_bond_other_d0.0010.025869
X-RAY DIFFRACTIONr_angle_refined_deg1.462.0028504
X-RAY DIFFRACTIONr_angle_other_deg0.788313425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82822.812224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85315863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1451551
X-RAY DIFFRACTIONr_chiral_restr0.0710.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021286
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_it0.9421.9413212
X-RAY DIFFRACTIONr_mcbond_other0.9431.9423211
X-RAY DIFFRACTIONr_mcangle_it1.4852.9074008
X-RAY DIFFRACTIONr_mcangle_other1.4852.9074009
X-RAY DIFFRACTIONr_scbond_it1.3232.1572972
X-RAY DIFFRACTIONr_scbond_other1.3232.1562971
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0793.1854497
X-RAY DIFFRACTIONr_long_range_B_refined5.07818.3957550
X-RAY DIFFRACTIONr_long_range_B_other5.07818.3987551
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 214 -
Rwork0.37 4209 -
obs--99.66 %
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)
11.92370.0313-0.46841.085-0.54081.57150.06710.02330.2246-0.06010.0614-0.1274-0.28670.1885-0.12860.0816-0.05640.0490.0672-0.03880.061258.292239.874332.5768
21.33930.3641-0.040.9364-0.20651.53960.0274-0.1897-0.09240.1283-0.0004-0.11950.14590.3144-0.0270.0410.036-0.0180.1093-0.01110.023956.733526.686946.0327
31.4665-0.3148-0.49180.89830.44041.73560.18650.1836-0.3122-0.1227-0.05830.02840.25420.0815-0.12820.12090.049-0.08940.1046-0.05750.101141.130611.01277.7809
42.1517-0.6017-0.56871.3021-0.3281.55530.1072-0.0453-0.3607-0.1414-0.02210.22480.1988-0.2329-0.08510.0542-0.0295-0.0530.06820.02780.088725.922114.854520.435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A245 - 448
2X-RAY DIFFRACTION2B245 - 448
3X-RAY DIFFRACTION3C252 - 448
4X-RAY DIFFRACTION4D250 - 448

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