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- PDB-6m34: Structural and functional insights into an Archaeal synthase -

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Basic information

Entry
Database: PDB / ID: 6m34
TitleStructural and functional insights into an Archaeal synthase
ComponentsDigeranylgeranylglyceryl phosphate synthase
KeywordsMEMBRANE PROTEIN / Lipid
Function / homology
Function and homology information


geranylgeranylglycerol-phosphate geranylgeranyltransferase / geranylgeranylglycerol-phosphate geranylgeranyltransferase activity / glycerophospholipid metabolic process / phospholipid 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
DIMETHYLALLYL DIPHOSPHATE / Chem-MPG / PHOSPHATE ION / Digeranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsWei, C. / Sixue, R.
CitationJournal: To Be Published
Title: Structural and mechanistic insights into the biosynthesis of Digeranylgeranylglyceryl phosphate synthase in membranes
Authors: Wei, C. / Sixue, R.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)65,93312
Polymers63,5712
Non-polymers2,36210
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-33 kcal/mol
Surface area28870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.500, 79.750, 70.300
Angle α, β, γ (deg.)90.000, 111.870, 90.000
Int Tables number5
Space group name H-MC121

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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)
References: UniProt: Q57727, geranylgeranylglycerol-phosphate geranylgeranyltransferase

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Non-polymers , 5 types, 10 molecules

#2: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Feature type: SUBJECT OF INVESTIGATION / Comment: LDAO, detergent*YM

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 200 mM NaCl, 20% (w/v) PEG400, and 200 mM Tris-HCl (pH 7.0).

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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: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.89→39.91 Å / Num. obs: 16504 / % possible obs: 99 % / Redundancy: 7.025 % / Biso Wilson estimate: 62.73 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.164 / Rrim(I) all: 0.178 / Χ2: 1.119 / Net I/σ(I): 9.65 / Num. measured all: 225465
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.89-3.077.2040.7142.9337663527352280.9320.7799.1
3.07-3.287.2270.4954.3235037486548480.9560.53499.7
3.28-3.547.1290.336.0432339454645360.9830.35699.8
3.54-3.886.9450.2168.6429219425142070.9880.23499
3.88-4.336.4560.14611.524105381137340.990.15998
4.33-4.997.2010.11116.9123763336833000.9930.1298
4.99-6.097.20.11914.4520117280827940.9930.12899.5
6.09-8.536.4410.07616.6614035222621790.9970.08397.9
8.53-39.917.2450.06226.929187128312680.9970.06798.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACT3.25data extraction
PDB_EXTRACTdata extraction
HKL-2000data collection
BUSTER2.10.3refinement
RefinementMethod to determine structure: SAD / Resolution: 2.9→39.91 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.842 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.394
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 826 5 %RANDOM
Rwork0.247 ---
obs0.248 16504 99.4 %-
Displacement parametersBiso max: 139.39 Å2 / Biso mean: 58.08 Å2 / Biso min: 31.91 Å2
Baniso -1Baniso -2Baniso -3
1--22.5189 Å20 Å2-9.3498 Å2
2--10.1824 Å20 Å2
3---12.3365 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: final / Resolution: 2.9→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 155 0 4603
Biso mean--77.81 --
Num. residues----560
LS refinement shellResolution: 2.9→2.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 41
RfactorNum. reflection% reflection
Rfree0.286 21 5.21 %
Rwork0.2623 382 -
all0.2634 403 -
obs--100 %

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