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- PDB-8g8p: F420-2/GTP(GDP) complex of F420-gamma glutamyl ligase (CofE) from... -

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Basic information

Entry
Database: PDB / ID: 8g8p
TitleF420-2/GTP(GDP) complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus
ComponentsCoenzyme F420:L-glutamate ligase
KeywordsLIGASE / ligase substrate complex
Function / homology
Function and homology information


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
Similarity search - Function
Coenzyme F420:L-glutamate ligase, archaeal / Coenzyme F420:L-glutamate ligase-like domain / Coenzyme F420:L-glutamate ligase / F420-0:Gamma-glutamyl ligase
Similarity search - Domain/homology
COENZYME F420 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / Coenzyme F420:L-glutamate ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBashiri, G. / Squire, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Poly-gamma-glutamylation of biomolecules.
Authors: Bashiri, G. / Bulloch, E.M.M. / Bramley, W.R. / Davidson, M. / Stuteley, S.M. / Young, P.G. / Harris, P.W.R. / Naqvi, M.S.H. / Middleditch, M.J. / Schmitz, M. / Chang, W.C. / Baker, E.N. / Squire, C.J.
History
DepositionFeb 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4479
Polymers27,4241
Non-polymers2,0248
Water2,270126
1
AAA: Coenzyme F420:L-glutamate ligase
hetero molecules

AAA: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,89518
Polymers54,8472
Non-polymers4,04816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557-x,y,-z+21
Buried area14290 Å2
ΔGint-150 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.238, 68.238, 91.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11AAA-504-

HOH

21AAA-508-

HOH

31AAA-525-

HOH

41AAA-526-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

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


Mass: 27423.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: cofE, AF_2256 / Production host: Escherichia coli (E. coli)
References: UniProt: O28028, coenzyme F420-0:L-glutamate ligase, coenzyme F420-1:gamma-L-glutamate ligase

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Non-polymers , 7 types, 134 molecules

#2: Chemical ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N5O18P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+, 1 mM F420-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.83→48.3 Å / Num. obs: 19796 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rpim(I) all: 0.039 / Net I/σ(I): 13.7
Reflection shellResolution: 1.83→1.88 Å / Num. unique obs: 990 / CC1/2: 0.599 / Rpim(I) all: 0.333 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→48.298 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.397 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2191 940 4.753 %
Rwork0.197 18835 -
all0.198 --
obs-19775 99.843 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.422 Å2
Baniso -1Baniso -2Baniso -3
1--0.031 Å20 Å20 Å2
2---0.031 Å2-0 Å2
3---0.061 Å2
Refinement stepCycle: LAST / Resolution: 1.83→48.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 122 126 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152030
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.6652889
X-RAY DIFFRACTIONr_angle_other_deg1.1671.5924676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.25220105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4711522
X-RAY DIFFRACTIONr_chiral_restr0.0480.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.1790.2366
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.21871
X-RAY DIFFRACTIONr_nbtor_refined0.1450.2982
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2116
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.225
X-RAY DIFFRACTIONr_nbd_other0.1860.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0910.225
X-RAY DIFFRACTIONr_mcbond_it1.0592.9321046
X-RAY DIFFRACTIONr_mcbond_other1.0542.9311045
X-RAY DIFFRACTIONr_mcangle_it1.6554.3971324
X-RAY DIFFRACTIONr_mcangle_other1.6544.3991325
X-RAY DIFFRACTIONr_scbond_it1.3013.0981086
X-RAY DIFFRACTIONr_scbond_other1.2263.11062
X-RAY DIFFRACTIONr_scangle_it1.9174.5771560
X-RAY DIFFRACTIONr_scangle_other1.9264.5771542
X-RAY DIFFRACTIONr_lrange_it3.20134.0462277
X-RAY DIFFRACTIONr_lrange_other3.15533.8862256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.8770.271820.2691328X-RAY DIFFRACTION98.1894
1.877-1.9280.277640.2431329X-RAY DIFFRACTION100
1.928-1.9840.235610.2221294X-RAY DIFFRACTION100
1.984-2.0450.273500.2311270X-RAY DIFFRACTION100
2.045-2.1120.234520.2281237X-RAY DIFFRACTION100
2.112-2.1860.226610.2231178X-RAY DIFFRACTION99.8388
2.186-2.2690.267590.2151131X-RAY DIFFRACTION100
2.269-2.3610.284520.2081118X-RAY DIFFRACTION100
2.361-2.4660.224520.2041060X-RAY DIFFRACTION100
2.466-2.5860.2520.2031009X-RAY DIFFRACTION100
2.586-2.7260.263410.225996X-RAY DIFFRACTION100
2.726-2.8910.214480.201916X-RAY DIFFRACTION100
2.891-3.090.303460.199871X-RAY DIFFRACTION100
3.09-3.3370.163300.186822X-RAY DIFFRACTION100
3.337-3.6550.18310.165763X-RAY DIFFRACTION99.8742
3.655-4.0850.18450.174678X-RAY DIFFRACTION100
4.085-4.7140.168450.147604X-RAY DIFFRACTION100
4.714-5.7670.221280.186543X-RAY DIFFRACTION100
5.767-8.1270.299260.207420X-RAY DIFFRACTION100
8.127-48.2980.209150.223268X-RAY DIFFRACTION99.6479

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