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- PDB-6t7n: Trypanosoma cruzi farnesyl diphosphate synthase in complex with I... -

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Basic information

Entry
Database: PDB / ID: 6t7n
TitleTrypanosoma cruzi farnesyl diphosphate synthase in complex with IPP and Mn
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / Farnesyl diphosphate synthase (FDPS) / Farnesyl pyrophosphate synthase (FPPS) / Trypanosoma cruzi / complex with IPP / Mn
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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / : / 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 in complex with IPP and Mn
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionOct 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 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

Downloads & links

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Assembly

Deposited unit
AAAA: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8626
Polymers41,2051
Non-polymers6575
Water2,990166
1
AAAA: Farnesyl diphosphate synthase
hetero molecules

AAAA: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,72512
Polymers82,4112
Non-polymers1,31410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area8830 Å2
ΔGint-80 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.450, 58.450, 391.793
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
Components on special symmetry positions
IDModelComponents
11AAAA-655-

HOH

21AAAA-664-

HOH

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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.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
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→50 Å / Num. obs: 58433 / % possible obs: 98.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.62 Å2 / CC1/2: 1 / Rsym value: 0.048 / Net I/σ(I): 35.46
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 2.69 / Num. unique obs: 8979 / CC1/2: 0.873 / Rsym value: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.01 Å / SU ML: 0.1695 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.7863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 2906 4.97 %
Rwork0.1735 55519 -
obs0.1752 58425 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 31 166 2978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952887
X-RAY DIFFRACTIONf_angle_d0.94383934
X-RAY DIFFRACTIONf_chiral_restr0.05444
X-RAY DIFFRACTIONf_plane_restr0.0065498
X-RAY DIFFRACTIONf_dihedral_angle_d12.42171704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.30841280.25822365X-RAY DIFFRACTION88.06
1.93-1.960.24171320.22982489X-RAY DIFFRACTION94.04
1.96-20.2331330.20242572X-RAY DIFFRACTION96.37
2-2.040.22331380.17342656X-RAY DIFFRACTION98.73
2.04-2.080.24221360.16652681X-RAY DIFFRACTION99.75
2.08-2.120.20431350.16612656X-RAY DIFFRACTION100
2.12-2.170.21421420.16192696X-RAY DIFFRACTION100
2.17-2.230.17871360.16092659X-RAY DIFFRACTION99.89
2.23-2.290.21361380.16062662X-RAY DIFFRACTION99.96
2.29-2.360.20461460.15652678X-RAY DIFFRACTION100
2.36-2.430.18921450.15352697X-RAY DIFFRACTION99.93
2.43-2.520.20161380.15622639X-RAY DIFFRACTION100
2.52-2.620.21611380.16292671X-RAY DIFFRACTION100
2.62-2.740.23491400.17822668X-RAY DIFFRACTION100
2.74-2.880.2061440.17432683X-RAY DIFFRACTION100
2.88-3.060.18331380.17532716X-RAY DIFFRACTION99.96
3.06-3.30.2161420.18452631X-RAY DIFFRACTION99.96
3.3-3.630.21161370.16982687X-RAY DIFFRACTION100
3.63-4.160.20631410.16272673X-RAY DIFFRACTION100
4.16-5.240.19311410.15362664X-RAY DIFFRACTION99.96
5.24-49.010.20631380.21012676X-RAY DIFFRACTION99.86
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)
10.24597672787-0.1312770844470.1783825829250.06222411866-0.07448870724310.0901634834095-0.0265100957754-0.143956476878-0.251257987902-0.01154571526510.0313358227717-0.1766463421520.08262601918380.225621473815-0.0001922454899820.2672743883010.0277833400099-0.03788550051280.2677681134780.02496513028580.3154938168795.7930283047714.952591608337.8743924552
20.294303189966-0.0071359179641-0.1172618167060.5453717758390.09153916993510.325525925572-0.137973753617-0.061665687631-0.126516606971-0.06518984263640.107298014885-0.06399501628790.193366146420.14060061713-5.87517838297E-60.2458791135110.00838718326968-0.006463071660630.2609442281630.01208669829290.2650128349213.4558159795215.775263281631.8486749362
30.100607866253-0.0584469233159-0.07790158305750.766393316179-0.0516335165580.00480636457855-0.1117853207640.168845737670.0186090313159-0.1029835904730.110089441006-0.0140355940630.04079350191260.06433074970441.60137584847E-50.275599473731-0.0309125663169-0.01637317995090.2682928571370.003237020027210.2421119317751.6833592124419.527508528528.5773856954
40.118149851244-0.0110731377228-0.1659944943480.278630646721-0.09296321811630.127187938186-0.0902330656944-0.147304542667-0.1086245969750.03550850661630.09065771258090.0769194393473-0.01569753459970.0638983526914-5.55277763137E-50.246970587377-0.0161783021147-0.01809594076650.2380156119890.02927466181850.303140590278-9.4224231530717.377531368234.4736034824
50.262691972210.2404530894170.1030237718660.4498868376070.06949667812230.704482240559-0.0282686555790.04910886420640.0278755064032-0.1328157927320.03655371870630.0288316105951-0.0582763233238-0.03703645466941.23108206911E-50.272572302676-0.0276746917891-0.01262490461540.2469150426680.006714332223190.254976902729-7.9690751398228.123589878418.2134496483
60.26237621365-0.1852087502210.03228527014070.150334839982-0.1249006422340.2533236665740.0915313528401-0.04040153614060.136052234413-0.2425321985310.009038717361010.2660266679230.0814437213819-0.00959480632629-0.0002137759467170.376761665136-0.0230663498854-0.007333462317370.2669492088140.01309887534890.262069092308-4.6735845617819.348804671710.3025880489
70.0869729668052-0.0890757011442-0.1780617927510.09369873866920.07008036844460.1989787073740.0243463367525-0.0887353694216-0.228185268837-0.2510929203070.08103591955690.3846645622590.316853473845-0.336522020576-3.26802455397E-50.418699607636-0.088961283333-0.09221147635370.3723257202510.05472108186940.412390187311-22.35283569513.02529051439.19551039783
80.817533892374-0.4387190542760.07115348300580.66950299189-0.01992230416770.2283818361730.2084316263140.39889993489-0.0965286933988-0.135468239459-0.0456535656870.05243867504190.1609883762590.09938451629060.03486922632920.392894796236-0.0272966580087-0.04832762311650.298392495603-0.02367373149420.254820663115-7.4301160789314.92471361892.95403645928
90.0199658630205-0.006850859149850.06870075072050.0406253109944-0.0992075316710.1455972354480.1284213281090.14140124284-0.408474955998-0.339449148274-0.0551720332012-0.2732880013670.08875599285290.06429869945231.22719254154E-50.4310548062530.01551171107890.01927749307190.290438338244-0.0123949623790.3143955033246.2421135368214.889058413611.1249797272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 231 )
6X-RAY DIFFRACTION6chain 'A' and (resid 232 through 256 )
7X-RAY DIFFRACTION7chain 'A' and (resid 257 through 301 )
8X-RAY DIFFRACTION8chain 'A' and (resid 302 through 342 )
9X-RAY DIFFRACTION9chain 'A' and (resid 343 through 362 )

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