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

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Basic information

Entry
Database: PDB / ID: 7tom
TitleX-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (GDGT-MAS) from Methanocaldococcus jannaschii with bacterial lipid substrate analog, 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 / : / Chem-LPP / METHIONINE / THIOCYANATE ION / IRON/SULFUR CLUSTER / 7,8-dihydro-6-hydroxymethylpterin dimethyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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)NIH (GM-122595 to S.J.B) 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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)62,60210
Polymers59,7351
Non-polymers2,8679
Water7,062392
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)55.609, 77.158, 112.817
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 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q58036, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 7 types, 401 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 genetically manipulated 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-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Thiocyanate, PEG 3350, 5'deoxyadenosine, 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: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 70348 / % possible obs: 98.6 % / Redundancy: 6.8 % / CC1/2: 0.988 / Net I/σ(I): 14.25
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 1962 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→45.54 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 3493 4.97 %
Rwork0.1502 66855 -
obs0.1526 70348 87.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.53 Å2 / Biso mean: 27.1698 Å2 / Biso min: 5.34 Å2
Refinement stepCycle: final / Resolution: 1.85→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 141 392 4492
Biso mean--32.86 34.66 -
Num. residues----498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.2626550.218968102332
1.87-1.90.2039760.20031425150147
1.9-1.930.2165910.19421800189158
1.93-1.960.2015980.17662013211166
1.96-1.990.22831250.17622243236873
1.99-2.020.24591280.16612365249378
2.02-2.060.24011250.17762576270185
2.06-2.10.21361480.17192720286890
2.1-2.140.21561550.16712937309295
2.14-2.190.18941530.16012939309297
2.19-2.240.22541560.14923004316098
2.24-2.30.22311530.15412978313198
2.3-2.360.22581550.14973001315698
2.36-2.430.20651570.14752992314997
2.43-2.510.20481520.15883003315597
2.51-2.60.22131470.15722852299995
2.6-2.70.19931530.16462871302494
2.7-2.820.2321590.151330623221100
2.82-2.970.21881560.156930603216100
2.97-3.160.2051620.15430443206100
3.16-3.40.23561550.148830483203100
3.4-3.740.1981610.13883044320599
3.75-4.290.14251560.12472998315498
4.29-5.40.15211550.12192858301394
5.4-45.540.16831620.145430543216100
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)
10.1997-0.12130.14580.56-0.16840.3429-0.02260.0985-0.2053-0.35940.0550.37250.2798-0.23940.07160.02070.01640.04090.06-0.07110.11193.60642.32524.713
20.79-0.31910.10091.0948-0.25160.5494-0.0760.03710.03440.17790.0123-0.1263-0.06660.0918-0.22760.0768-0.0148-0.0220.0719-0.01170.03919.88553.62839.124
30.04270.0322-0.03120.0403-0.03510.4208-0.059-0.2276-0.19770.25730.08160.06920.22520.19260.02950.31970.07090.01690.20050.05740.193818.95632.27651.523
40.3843-0.0828-0.13150.08360.00410.1644-0.05760.23150.0596-0.0870.0680.0708-0.0947-0.1311-0.00450.10160.0207-0.00120.06510.03580.08876.56261.58832.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:86 )A-2 - 86
2X-RAY DIFFRACTION2( CHAIN A AND RESID 87:351 )A87 - 351
3X-RAY DIFFRACTION3( CHAIN A AND RESID 352:439 )A352 - 439
4X-RAY DIFFRACTION4( CHAIN A AND ( RESID 440:501 OR RESID 601:606 ) )A440 - 501
5X-RAY DIFFRACTION4( CHAIN A AND ( RESID 440:501 OR RESID 601:606 ) )A601 - 606

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