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- PDB-6sfa: Trypanosoma cruzi farnesyl diphosphate synthase apo structure wit... -

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Basic information

Entry
Database: PDB / ID: 6sfa
TitleTrypanosoma cruzi farnesyl diphosphate synthase apo structure with Mn ions
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / Farnesyl diphosphate synthase (FDPS) / Farnesyl pyrophosphate synthase (FPPS) / Trypanosoma cruzi / Mn ions
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
: / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Union
CitationJournal: To Be Published
Title: Trypanosoma cruzi farnesyl diphosphate synthase apo structure with Mn ions
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionAug 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 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: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4114
Polymers41,2051
Non-polymers2063
Water3,135174
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8238
Polymers82,4112
Non-polymers4126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6790 Å2
ΔGint-91 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.746, 57.746, 397.563
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Farnesyl diphosphate synthase


Mass: 41205.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WS26
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 4mM ZnSO4+ 8 mM MES pH:6.50, 12.36% PEG MME 550, 11.57% Glycerol. crystal obtained by microseeding: 160mM (NH4)2SO4, 80mM NaOAc pH:5.00, 20% PEG 4000, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.893174 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.893174 Å / Relative weight: 1
ReflectionResolution: 1.9→49.69 Å / Num. obs: 57642 / % possible obs: 98.4 % / Redundancy: 7.6 % / Biso Wilson estimate: 30.25 Å2 / CC1/2: 0.996 / Rsym value: 0.074 / Net I/σ(I): 24.24
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 8564 / CC1/2: 0.875 / Rsym value: 0.5 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.62 Å / SU ML: 0.1968 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.2396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2017 2873 4.98 %
Rwork0.1673 54764 -
obs0.1691 57637 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 7 174 2934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962846
X-RAY DIFFRACTIONf_angle_d0.96973882
X-RAY DIFFRACTIONf_chiral_restr0.052441
X-RAY DIFFRACTIONf_plane_restr0.0061497
X-RAY DIFFRACTIONf_dihedral_angle_d12.0771672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.28011150.25662224X-RAY DIFFRACTION81.5
1.93-1.960.28531270.21742413X-RAY DIFFRACTION92.77
1.96-20.23651290.19432515X-RAY DIFFRACTION93.39
2-2.040.21291380.17392633X-RAY DIFFRACTION99.68
2.04-2.080.20981390.16222625X-RAY DIFFRACTION100
2.08-2.120.19731430.15492669X-RAY DIFFRACTION100
2.12-2.170.18591340.14662604X-RAY DIFFRACTION100
2.17-2.230.21971420.14132690X-RAY DIFFRACTION99.96
2.23-2.290.20471330.14692616X-RAY DIFFRACTION100
2.29-2.360.16151450.1492616X-RAY DIFFRACTION100
2.36-2.430.2131370.15282679X-RAY DIFFRACTION100
2.43-2.520.18371350.14682672X-RAY DIFFRACTION99.96
2.52-2.620.18791340.14452648X-RAY DIFFRACTION100
2.62-2.740.19941380.14862646X-RAY DIFFRACTION100
2.74-2.880.18141470.16622657X-RAY DIFFRACTION100
2.88-3.060.21841380.17362630X-RAY DIFFRACTION100
3.06-3.30.20371320.1782627X-RAY DIFFRACTION100
3.3-3.630.19891390.16972673X-RAY DIFFRACTION100
3.63-4.160.19861380.15512646X-RAY DIFFRACTION100
4.16-5.240.161460.15412651X-RAY DIFFRACTION100
5.24-49.620.25491440.21592630X-RAY DIFFRACTION99.93
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)
11.131061065540.1470564411040.3244592949680.512790193668-0.008870823916740.468426401912-0.0586651519866-0.03992457182170.190330583387-0.00153387401240.01144398569910.0493037738665-0.0193933961553-0.0323951311455-3.58747683387E-70.197471400758-0.01636062156520.007913189554930.220968325469-0.01411218052970.24219010318832.691233916432.917924927731.8055427655
20.670149805259-0.269907078004-0.3875669173510.4974942996860.08750365613360.682932133011-0.003695386594950.1436189846370.154020881503-0.1172656486520.0347772478307-0.0945818552538-0.11190598845-0.001626936446881.12217497713E-60.317260211473-0.02704548540820.0121817051510.3543898117910.0224401802860.27789618217142.802520254831.81684865269.4107962661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 171 )
2X-RAY DIFFRACTION2chain 'A' and (resid 172 through 358 )

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