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- PDB-6sf8: Trypanosoma cruzi farnesyl diphosphate synthase in complex with f... -

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Basic information

Entry
Database: PDB / ID: 6sf8
TitleTrypanosoma cruzi farnesyl diphosphate synthase in complex with fragment j51
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / Farnesyl diphosphate synthase (FDPS) / Farnesyl pyrophosphate synthase (FPPS) / Trypanosoma cruzi / complex with fragment
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
Chem-47Y / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Union
CitationJournal: To Be Published
Title: Trypanosoma cruzi farnesyl diphosphate synthase in complex with fragment j51
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 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)41,5503
Polymers41,2051
Non-polymers3442
Water5,098283
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1006
Polymers82,4112
Non-polymers6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area6290 Å2
ΔGint-74 kcal/mol
Surface area27980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.903, 57.903, 398.288
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-47Y / 3-[(4E)-4-imino-5,6-dimethylfuro[2,3-d]pyrimidin-3(4H)-yl]-N,N-dimethylpropan-1-amine


Mass: 248.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 180mM (NH4)2SO4, 80mM NaOAc pH:5.50 20% PEG 4000, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.62→48.63 Å / Num. obs: 52291 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 22.25 Å2 / CC1/2: 1 / Rsym value: 0.05 / Net I/σ(I): 35.16
Reflection shellResolution: 1.62→1.72 Å / Mean I/σ(I) obs: 3.47 / Num. unique obs: 8151 / CC1/2: 0.916 / Rsym value: 0.483 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yhl

1yhl


Resolution: 1.62→48.63 Å / SU ML: 0.1892 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.3479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1916 2615 5 %
Rwork0.1732 49674 -
obs0.1741 52289 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.62 Å2
Refinement stepCycle: LAST / Resolution: 1.62→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 18 283 3110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842954
X-RAY DIFFRACTIONf_angle_d0.92464032
X-RAY DIFFRACTIONf_chiral_restr0.0531450
X-RAY DIFFRACTIONf_plane_restr0.006534
X-RAY DIFFRACTIONf_dihedral_angle_d12.22281752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.3531310.35762492X-RAY DIFFRACTION98.17
1.65-1.680.27011330.25722517X-RAY DIFFRACTION99.92
1.68-1.710.26031340.20242551X-RAY DIFFRACTION99.85
1.71-1.750.21311350.17352559X-RAY DIFFRACTION99.85
1.75-1.790.21541350.16482563X-RAY DIFFRACTION100
1.79-1.840.20681320.16352521X-RAY DIFFRACTION99.96
1.84-1.890.22781360.16642577X-RAY DIFFRACTION99.89
1.89-1.940.20831360.17192587X-RAY DIFFRACTION99.96
1.94-20.20661360.1682578X-RAY DIFFRACTION99.96
2-2.080.20031360.1642585X-RAY DIFFRACTION100
2.08-2.160.17481350.15482571X-RAY DIFFRACTION100
2.16-2.260.18591370.15522599X-RAY DIFFRACTION100
2.26-2.380.15371370.14922601X-RAY DIFFRACTION100
2.38-2.530.18961390.15652646X-RAY DIFFRACTION99.93
2.53-2.720.20451380.16322622X-RAY DIFFRACTION100
2.72-2.990.17481400.16992659X-RAY DIFFRACTION99.96
2.99-3.430.20441420.17482700X-RAY DIFFRACTION99.96
3.43-4.320.16821450.16612746X-RAY DIFFRACTION100
4.32-48.630.18851580.19283000X-RAY DIFFRACTION99.94
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)
10.9570686880820.1726590037570.2649187682380.3361020681830.1594977353510.806641917695-0.07277311060570.04510630610680.164056771005-0.02010178716440.000909184767156-0.00651445191281-0.09069046502020.0493850432647-0.0001612185385550.1317990343420.008247887161050.006621543922980.1419230112160.03247773119380.173597448999-3.73329615929-14.7844597219-32.8988100782
20.760053504795-0.029512767015-0.4266561083950.281044020263-0.06693876266230.8007576044070.0139928997735-0.09224165097810.120360624220.02753662270770.01989286056190.0254767457653-0.07497505920120.00827139572189-4.09567787783E-50.1631007181050.01306321235460.001927827229190.225319799055-0.01187389895360.181037299453-12.7413842859-19.5106372969-11.9490612659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 361 )

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