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- PDB-7vqd: Structure of MA1831 from Methanosarcina acetivorans in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7vqd
TitleStructure of MA1831 from Methanosarcina acetivorans in complex with farnesyl pyrophosphate and geranylgeranyl pyrophosphate.
ComponentsDi-trans-poly-cis-decaprenylcistransferase
KeywordsTRANSFERASE / cis-prenyltransferase
Function / homologypolyprenol biosynthetic process / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / transferase activity, transferring alkyl or aryl (other than methyl) groups / metal ion binding / NerylNeryl pyrophosphate / FARNESYL DIPHOSPHATE / Di-trans-poly-cis-decaprenylcistransferase
Function and homology information
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsZhang, L.L. / Chen, C.C. / Liu, W.D. / Huang, J.W. / Zhang, X.W. / Liu, B.B. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structural insights to a bi-functional isoprenyl diphosphate synthase that can catalyze head-to-tail and head-to-middle condensation.
Authors: Zhang, L. / Zhang, X. / Min, J. / Liu, B. / Huang, J.W. / Yang, Y. / Liu, W. / Dai, L. / Yang, Y. / Chen, C.C. / Guo, R.T.
History
DepositionOct 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: Di-trans-poly-cis-decaprenylcistransferase
B: Di-trans-poly-cis-decaprenylcistransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5785
Polymers51,6492
Non-polymers9293
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-35 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.061, 81.581, 59.755
Angle α, β, γ (deg.)90.000, 102.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Di-trans-poly-cis-decaprenylcistransferase


Mass: 25824.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (archaea)
Gene: uppS, MA_1831 / Plasmid: pET-32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TPS4
#2: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BUE / NerylNeryl pyrophosphate


Mass: 450.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.5M ammonium sulfate, 0.1M Tris (pH 8.0), 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.39→33.43 Å / Num. obs: 20642 / % possible obs: 91.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 6.5
Reflection shellResolution: 2.39→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.855 / Num. unique obs: 2369 / % possible all: 43.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CAQ

7caq


Resolution: 2.39→33.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.32 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 958 5.1 %RANDOM
Rwork0.171 ---
obs0.175 17900 91.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 28.17 Å2 / Biso min: 4.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.24 Å2
2--0.15 Å20 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 2.39→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 58 323 3730
Biso mean--54.89 31.85 -
Num. residues----408
LS refinement shellResolution: 2.39→2.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 73 -
Rwork0.282 1180 -
all-1253 -
obs--81.84 %

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