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- PDB-7tol: X-ray crystal structure of glycerol dibiphytanyl glycerol tetraet... -

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Basic information

Entry
Database: PDB / ID: 7tol
TitleX-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (GDGT-MAS) from Methanocaldococcus jannaschii with archaeal lipid, 5'deoxyadenosine, and methionine bound
Componentsglycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase
KeywordsOXIDOREDUCTASE / Radical SAM Enzyme / Biphytanyl Chain / Glycerol dibiphytanyl glycerol tetraether / Archaeal Lipid modification / [4Fe-4S] cluster / Rubredoxin
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / 4 iron, 4 sulfur cluster binding / methylation / metal ion binding
Similarity search - Function
7,8-dihydro-6-hydroxymethylpterin dimethylase / Methyltransferase, class D / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
5'-DEOXYADENOSINE / : / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / Chem-L4P / METHIONINE / TRIETHYLENE GLYCOL / IRON/SULFUR CLUSTER / 7,8-dihydro-6-hydroxymethylpterin dimethyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsLloyd, C.T. / Booker, S.J. / Boal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)0000-0002-1234-8472 United States
Howard Hughes Medical Institute (HHMI)Squire J. Booker United States
CitationJournal: Nature / Year: 2022
Title: Discovery, structure and mechanism of a tetraether lipid synthase.
Authors: Lloyd, C.T. / Iwig, D.F. / Wang, B. / Cossu, M. / Metcalf, W.W. / Boal, A.K. / Booker, S.J.
History
DepositionJan 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,93710
Polymers59,7351
Non-polymers3,2029
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration was performed to isolate monomeric GDGTs.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.999, 77.598, 117.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase / 7 / 8-dihydro-6-hydroxymethylpterin dimethyltransferase / 6-hydroxymethyl-H(2)pterin dimethyltransferase


Mass: 59735.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 20 residues are from a tag and are denoted with negative numbers. The 21st residue, methionine, is the start of the native protein and has sequence number 1
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0619 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q58036, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 8 types, 202 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-L1P / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO-3-PHOSPHATE


Mass: 733.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H89O6P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-L4P / 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL


Mass: 807.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H95O8P / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, PEG 300, 5'deoxyadenosine and methionine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 53752 / % possible obs: 98.5 % / Redundancy: 3.9 % / CC1/2: 0.987 / Net I/σ(I): 19.25
Reflection shellResolution: 2.03→2.07 Å / Num. unique obs: 1666 / CC1/2: 0.656

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TOM

7tom


Resolution: 2.03→46.84 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 3363 6.26 %
Rwork0.1865 50389 -
obs0.1892 53752 82.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.64 Å2 / Biso mean: 36.5147 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 2.03→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 167 193 4283
Biso mean--36.85 36.29 -
Num. residues----493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.060.3215560.216379084631
2.06-2.090.254680.2296975104338
2.09-2.120.2601760.23531132120845
2.12-2.160.28031060.21961491159759
2.16-2.20.24021070.22821673178066
2.2-2.240.24541310.20911883201474
2.24-2.280.26231280.2222008213679
2.28-2.320.27641440.22032164230886
2.32-2.380.24171460.21562335248190
2.38-2.430.25431570.20572311246893
2.43-2.490.27941540.20572368252293
2.49-2.560.21831560.20262377253393
2.56-2.630.25971600.19962404256495
2.63-2.720.27721620.19372494265697
2.72-2.820.20011680.19242474264297
2.82-2.930.22471630.19942426258996
2.93-3.060.23411660.19972432259897
3.06-3.220.26111660.18812440260695
3.22-3.430.25531570.18392406256395
3.43-3.690.2141620.17342334249692
3.69-4.060.20411530.16062334248792
4.06-4.650.17971450.15152231237689
4.65-5.850.18361640.15912446261096
5.86-46.840.23051680.18332461262997
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)
10.3044-0.10330.16950.0691-0.02890.152-0.00760.02980.08470.0328-0.02360.07250.00540.0004-0.00220.13740.0022-0.01250.09990.02160.14846.2159.26433.013
28.7866-3.05917.46666.9063-4.83067.19710.3422-0.2456-0.2350.0858-0.0694-0.06210.3814-0.0934-0.27370.40350.0482-0.17250.47090.04150.370618.99359.00335.481
30.41050.15430.15740.42170.0860.16910.01310.1114-0.3009-0.1526-0.02270.31150.2077-0.0523-0.00190.19010.01250.01370.1014-0.01370.20243.49740.41125.865
40.96440.11640.47011.29450.02640.59750.01660.0630.01060.4202-0.064-0.34110.00310.2918-0.070.07190.0346-0.05810.20620.04440.081820.16853.439.572
50.1684-0.00780.21050.09090.00190.19920.4255-0.7091-0.76860.9037-0.1-0.30370.63860.15860.33040.73410.1131-0.32270.28630.4030.314817.96532.7551.272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 440:499 )A440 - 499
2X-RAY DIFFRACTION2( CHAIN A AND RESID 606:606 )A606
3X-RAY DIFFRACTION3( CHAIN A AND RESID -1:86 )A-1 - 86
4X-RAY DIFFRACTION4( CHAIN A AND RESID 87:325 )A87 - 325
5X-RAY DIFFRACTION5( CHAIN A AND RESID 326:439 )A326 - 439

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