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

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Basic information

Entry
Database: PDB / ID: 6sdp
TitleTrypanosoma cruzi farnesyl diphosphate synthase in complex with fragment 4np
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 / membrane / metal ion binding / 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
P-NITROPHENOL / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 4np
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 29, 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

Downloads & links

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Assembly

Deposited unit
A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5715
Polymers41,2051
Non-polymers3664
Water4,702261
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,14310
Polymers82,4112
Non-polymers7328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7570 Å2
ΔGint-185 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.864, 57.864, 397.732
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
11A-757-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.45→397.732 Å / Num. obs: 71867 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.998 / Rsym value: 0.064 / Net I/σ(I): 26.5
Reflection shellResolution: 1.45→1.54 Å / Mean I/σ(I) obs: 4.54 / Num. unique obs: 11311 / CC1/2: 0.946 / Rsym value: 0.485 / % possible all: 100

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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: 1.45→49.72 Å / SU ML: 0.1234 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 15.2999
RfactorNum. reflection% reflection
Rfree0.1881 3593 5 %
Rwork0.1668 --
obs0.1678 71864 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.41 Å2
Refinement stepCycle: LAST / Resolution: 1.45→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 17 261 3112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782963
X-RAY DIFFRACTIONf_angle_d0.91954038
X-RAY DIFFRACTIONf_chiral_restr0.0703451
X-RAY DIFFRACTIONf_plane_restr0.0065530
X-RAY DIFFRACTIONf_dihedral_angle_d18.21021062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.23141330.22372531X-RAY DIFFRACTION99.92
1.47-1.490.2141360.19592571X-RAY DIFFRACTION100
1.49-1.510.22261330.19152539X-RAY DIFFRACTION100
1.51-1.530.22611360.18212585X-RAY DIFFRACTION100
1.53-1.560.21291360.17572568X-RAY DIFFRACTION99.96
1.56-1.580.15011330.17312534X-RAY DIFFRACTION100
1.58-1.610.18691370.17182611X-RAY DIFFRACTION100
1.61-1.640.19971340.16842545X-RAY DIFFRACTION100
1.64-1.670.16311360.16152585X-RAY DIFFRACTION100
1.67-1.710.19441370.17032601X-RAY DIFFRACTION100
1.71-1.740.20071350.1732561X-RAY DIFFRACTION100
1.74-1.780.19641350.17092572X-RAY DIFFRACTION100
1.78-1.830.16091370.16922595X-RAY DIFFRACTION100
1.83-1.880.19681360.16652592X-RAY DIFFRACTION100
1.88-1.930.16821400.16452651X-RAY DIFFRACTION100
1.93-1.990.15961350.16442573X-RAY DIFFRACTION99.96
1.99-2.070.17961390.16272634X-RAY DIFFRACTION100
2.07-2.150.18591370.15782608X-RAY DIFFRACTION100
2.15-2.250.19041380.1522622X-RAY DIFFRACTION100
2.25-2.360.1691380.14892624X-RAY DIFFRACTION100
2.36-2.510.16671420.15322684X-RAY DIFFRACTION100
2.51-2.710.1941390.15462649X-RAY DIFFRACTION99.96
2.71-2.980.14781420.16122694X-RAY DIFFRACTION100
2.98-3.410.19771440.17092739X-RAY DIFFRACTION100
3.41-4.30.20761460.15472765X-RAY DIFFRACTION100
4.3-49.720.20481590.19213038X-RAY DIFFRACTION99.97
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)
10.4418900073250.0795273576928-0.2956048993680.298456470003-0.2503734649690.280850615913-0.03257731472650.2549369121160.0630046501397-0.069579077790.0436064369078-0.184755843788-0.1361501680520.327387836496-5.37040562011E-50.147683451123-0.002810749306630.002304016321340.1836588040790.02762157702310.1794711624094.22544531716-13.1500368798-38.1758800651
20.7472793227190.0608411021891-0.01212355910440.3067820446450.07900505286030.436643368595-0.0156011036747-0.01258749600350.0697429656845-0.008911930582510.00763417570726-0.0286269892095-0.02537946609720.0342403336541-1.39527500464E-50.118619767580.006817371531180.006439477531020.1376174601990.02146691103840.1610550840470.56847163193-15.9210227388-30.723255875
30.463339335082-0.1479752776480.2063561377490.462608425986-0.001982637433040.7386837875260.0146685571719-0.006639023024820.0471002271526-0.0024048144939-0.00982152115720.00088437997631-0.0286315157041-0.0206671122415-1.6727811798E-50.1249574126390.008659193754260.01253202865370.1290851617050.01511373263350.156082523828-8.68539842601-21.0471946655-30.8881567141
40.170220294949-0.039897388384-0.06753680783650.2317604530820.01215454039710.4054349520710.0158859798115-0.0411610327264-0.008460689180770.0265697552946-0.02290704673110.02849410267770.0135353717281-0.04524001395213.72261991248E-60.1633866890080.01372813662860.008289911710840.1943748962750.009339612203460.150386932232-13.2309131693-26.0406641799-14.9227084644
50.2670601682210.2315233209830.05672756774320.1838104890610.05213642550620.3242937113850.112573608576-0.09266027629770.0605390728198-0.0502705111157-0.005704538190530.06867110471690.0101413446125-0.0514449849903-0.0001219245339840.2225257321060.00242824815073-0.002413090696270.243743366249-0.009350891905630.205237532429-7.24492179229-18.147362653-10.2260061276
60.2767744041440.3153187448830.1965187616630.2825039242450.1268945520320.216556695116-0.07958092324290.07144147177870.2094964097720.06320547819350.1151365823280.178096103216-0.297091597476-0.0651366961459-0.0008213300107090.2246070645460.03406969110150.0127788463670.2819183443220.02954897657640.245814469702-25.4091519445-12.3665398157-8.34365509361
70.7866312675920.2563136643760.1538188592780.493157169956-0.198055925210.7144737772930.0612128413846-0.42673934080.3064658395570.01971765749060.0273109954219-0.0155927711894-0.213986408620.1443717679020.03277070331720.1987481439860.002734262908810.01205516013410.237906029786-0.04376183641490.180126385897-5.04496514481-14.5987230462-4.97498176351
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 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 231 )
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 256 )
6X-RAY DIFFRACTION6chain 'A' and (resid 257 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 360 )

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