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- PDB-7uld: GTP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglob... -

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Basic information

Entry
Database: PDB / ID: 7uld
TitleGTP 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
CARBONATE ION / GUANOSINE-5'-TRIPHOSPHATE / : / Coenzyme F420:L-glutamate ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)28,4289
Polymers27,4241
Non-polymers1,0048
Water3,639202
1
A: Coenzyme F420:L-glutamate ligase
hetero molecules

A: Coenzyme F420:L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,85618
Polymers54,8472
Non-polymers2,00816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557-x,y,-z+21
Buried area10930 Å2
ΔGint-180 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.544, 68.544, 93.243
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-509-

HOH

21A-556-

HOH

31A-566-

HOH

41A-599-

HOH

51A-600-

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 , 6 types, 210 molecules

#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 202 / 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 Å3/Da / Density % sol: 38.4 %
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+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→46.6 Å / Num. obs: 55332 / % possible obs: 100 % / Redundancy: 28 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 12.3
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 27.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2692 / CC1/2: 0.517 / Rpim(I) all: 0.693 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2phn

2phn


Resolution: 1.3→43.04 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.112 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.049
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 2734 4.9 %RANDOM
Rwork0.1557 ---
obs0.157 52542 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.57 Å2 / Biso mean: 17.499 Å2 / Biso min: 8.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å20 Å2
2---0.22 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.3→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 54 202 2134
Biso mean--25.75 31.15 -
Num. residues----247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132012
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171954
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.6372731
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5794521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.221.275102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59115359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0631519
X-RAY DIFFRACTIONr_chiral_restr0.0680.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_rigid_bond_restr0.96833958
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 197 -
Rwork0.261 3830 -
all-4027 -
obs--99.93 %

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