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- PDB-6m31: Structural and Functional Insights into an Archaeal Lipid Synthase -

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Basic information

Entry
Database: PDB / ID: 6m31
TitleStructural and Functional Insights into an Archaeal Lipid Synthase
ComponentsDigeranylgeranylglyceryl phosphate synthase
KeywordsMEMBRANE PROTEIN / Lipid
Function / homology
Function and homology information


geranylgeranylglycerol-phosphate geranylgeranyltransferase / geranylgeranylglycerol-phosphate geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Digeranylgeranylglyceryl phosphate synthase / : / UbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family
Similarity search - Domain/homology
Chem-MPG / PHOSPHATE ION / Digeranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsRen, S. / Cheng, W.
CitationJournal: Cell Rep / Year: 2020
Title: Structural and Functional Insights into an Archaeal Lipid Synthase
Authors: Ren, S. / de Kok, N.A. / Gu, Y. / Yan, W. / Sun, Q. / Chen, Y. / He, J. / Tian, L. / Andringa, R.L. / Zhu, X. / Tang, M. / Qi, S. / Xu, H. / Ren, H. / Fu, X. / Minnaard, A.J. / Yang, S. / ...Authors: Ren, S. / de Kok, N.A. / Gu, Y. / Yan, W. / Sun, Q. / Chen, Y. / He, J. / Tian, L. / Andringa, R.L. / Zhu, X. / Tang, M. / Qi, S. / Xu, H. / Ren, H. / Fu, X. / Minnaard, A.J. / Yang, S. / Zhang, W. / Li, W. / Wei, Y. / Driessen, A.J. / Cheng, W.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Aug 17, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Digeranylgeranylglyceryl phosphate synthase
B: Digeranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,78950
Polymers63,5712
Non-polymers12,21748
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25390 Å2
ΔGint52 kcal/mol
Surface area28890 Å2
Unit cell
Length a, b, c (Å)70.000, 133.490, 79.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Digeranylgeranylglyceryl phosphate synthase / DGGGPS / (S)-2 / 3-di-O-geranylgeranylglyceryl phosphate synthase / Geranylgeranylglycerol- ...DGGGPS / (S)-2 / 3-di-O-geranylgeranylglyceryl phosphate synthase / Geranylgeranylglycerol-phosphate geranylgeranyltransferase


Mass: 31785.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MJ0279 / Production host: Escherichia coli ATCC 8739 (bacteria) / Strain (production host): ATCC 8739
References: UniProt: Q57727, geranylgeranylglycerol-phosphate geranylgeranyltransferase

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Non-polymers , 5 types, 91 molecules

#2: Chemical...
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C14H31NO / Feature type: SUBJECT OF INVESTIGATION / Comment: LDAO, detergent*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 200 mM NaCl, 20% (w/v) PEG500, and 200 mM Tris-HCl (pH 8.0).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→48.89 Å / Num. obs: 33780 / % possible obs: 99.8 % / Redundancy: 6.904 % / Biso Wilson estimate: 45.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Χ2: 1.221 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.29-2.436.9740.7732.63102850.930.83499.5
2.43-2.66.7130.5243.7696820.9620.56899.8
2.6-2.817.1910.3475.7790290.9870.37499.8
2.81-3.086.8690.2188.5383140.9930.23699.9
3.08-3.446.9660.12213.5775320.9970.13299.9
3.44-3.976.9620.07266180.9990.078100

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Processing

Software
NameVersionClassification
SHELXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.289 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1689 5 %RANDOM
Rwork0.201 ---
obs0.202 33780 99.8 %-
Displacement parametersBiso max: 145.39 Å2 / Biso mean: 54.73 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-8.2408 Å20 Å20 Å2
2---15.7522 Å20 Å2
3---7.5114 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.3→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 845 43 5336
Biso mean--80.86 55.6 -
Num. residues----560
LS refinement shellResolution: 2.3→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3206 34 5.03 %
Rwork0.2379 642 -
all0.2419 676 -
obs--99.42 %

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