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- PDB-7ule: F420-1/GDP complex of F420-gamma glutamyl ligase (CofE) from Arch... -

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Basic information

Entry
Database: PDB / ID: 7ule
TitleF420-1/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
Chem-F4I / GUANOSINE-5'-DIPHOSPHATE / : / Coenzyme F420:L-glutamate ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionApr 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6446
Polymers27,4241
Non-polymers1,2215
Water2,450136
1
A: Coenzyme F420:L-glutamate ligase
hetero molecules

A: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,28812
Polymers54,8472
Non-polymers2,44110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557-x,y,-z+21
Buried area10200 Å2
ΔGint-114 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.082, 69.082, 92.352
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
11A-498-

HOH

21A-515-

HOH

31A-535-

HOH

41A-536-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 , 5 types, 141 molecules

#2: 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
#3: Chemical ChemComp-F4I / (2~{S})-2-[[(2~{S})-2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[2,4,8-tris(oxidanylidene)-1,9-dihydropyrimido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxypropanoyl]amino]pentanedioic acid / Coeznyme F420-1


Mass: 644.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N4O15P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.01 Å3/Da / Density % sol: 38.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+, 1 mM F420-1

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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: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.7→48.9 Å / Num. obs: 25326 / % possible obs: 100 % / Redundancy: 26.7 % / CC1/2: 0.998 / Rpim(I) all: 0.019 / Net I/σ(I): 18.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 27.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1320 / CC1/2: 0.538 / Rpim(I) all: 0.653 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PHN

2phn


Resolution: 1.7→48.896 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.218 / SU B: 3.129 / SU ML: 0.099 / Average fsc free: 0.8901 / Average fsc work: 0.9038 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1274 5.039 %RANDOM
Rwork0.2097 24009 --
all0.211 ---
obs-25283 99.968 %-
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: 35.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.018 Å2-0 Å20 Å2
2---0.018 Å20 Å2
3---0.036 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 75 136 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131978
X-RAY DIFFRACTIONr_bond_other_d0.0360.0151882
X-RAY DIFFRACTIONr_angle_refined_deg1.311.6592664
X-RAY DIFFRACTIONr_angle_other_deg2.9871.5884319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.9820.99101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77615324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.141519
X-RAY DIFFRACTIONr_chiral_restr0.0470.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02427
X-RAY DIFFRACTIONr_nbd_refined0.1750.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.21717
X-RAY DIFFRACTIONr_nbtor_refined0.1450.2962
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2660.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.229
X-RAY DIFFRACTIONr_nbd_other0.1890.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.219
X-RAY DIFFRACTIONr_mcbond_it1.2173.772999
X-RAY DIFFRACTIONr_mcbond_other1.2153.769995
X-RAY DIFFRACTIONr_mcangle_it1.8895.6551247
X-RAY DIFFRACTIONr_mcangle_other1.8885.6551247
X-RAY DIFFRACTIONr_scbond_it1.433.927977
X-RAY DIFFRACTIONr_scbond_other1.4183.931969
X-RAY DIFFRACTIONr_scangle_it2.2415.8321417
X-RAY DIFFRACTIONr_scangle_other2.245.8311418
X-RAY DIFFRACTIONr_lrange_it3.30543.2222138
X-RAY DIFFRACTIONr_lrange_other3.26243.0142117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3551010.3291750X-RAY DIFFRACTION99.8921
1.792-1.8440.331820.2941666X-RAY DIFFRACTION99.9428
1.844-1.9010.328760.2591590X-RAY DIFFRACTION99.94
1.901-1.9630.305780.261575X-RAY DIFFRACTION99.9395
1.963-2.0320.285650.2591530X-RAY DIFFRACTION100
2.032-2.1080.295920.241437X-RAY DIFFRACTION100
2.108-2.1940.261770.2241398X-RAY DIFFRACTION100
2.194-2.2920.263830.2271346X-RAY DIFFRACTION100
2.292-2.4030.27670.211312X-RAY DIFFRACTION100
2.403-2.5330.279600.2141238X-RAY DIFFRACTION100
2.533-2.6870.227620.2171171X-RAY DIFFRACTION100
2.687-2.8720.265680.2071102X-RAY DIFFRACTION100
2.872-3.1020.225550.2011030X-RAY DIFFRACTION100
3.397-3.7970.229460.193868X-RAY DIFFRACTION100
3.797-4.3820.189440.183790X-RAY DIFFRACTION100
4.382-5.3610.189360.171674X-RAY DIFFRACTION100
5.361-7.5590.225320.208541X-RAY DIFFRACTION100

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