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- PDB-6r36: T. brucei farnesyl pyrophosphate synthase (FPPS) -

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Basic information

Entry
Database: PDB / ID: 6r36
TitleT. brucei farnesyl pyrophosphate synthase (FPPS)
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / sterol biosynthesis / farnesyl diphosphate synthase / Trypanosoma brucei / homodimer
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsMuenzker, L. / Petrick, J.K. / Schleberger, C. / Jahnke, W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675899 Switzerland
CitationJournal: Chembiochem / Year: 2020
Title: Fragment-Based Discovery of Non-bisphosphonate Binders of Trypanosoma brucei Farnesyl Pyrophosphate Synthase.
Authors: Munzker, L. / Petrick, J.K. / Schleberger, C. / Clavel, D. / Cornaciu, I. / Wilcken, R. / Marquez, J.A. / Klebe, G. / Marzinzik, A. / Jahnke, W.
History
DepositionMar 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4324
Polymers42,1691
Non-polymers2623
Water1,45981
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8638
Polymers84,3382
Non-polymers5256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6800 Å2
ΔGint-14 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.490, 60.490, 340.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 42169.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GP is an expression tag / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86C09
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: needles
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Cesium chloride, 12 %w/v PEG 3350, 12 % v/v DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99974 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99974 Å / Relative weight: 1
ReflectionResolution: 1.668→52.384 Å / Num. obs: 28487 / % possible obs: 63.8 % / Redundancy: 18.3 % / Biso Wilson estimate: 29.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.022 / Rrim(I) all: 0.094 / Rsym value: 0.091 / Net I/σ(I): 21.7
Reflection shellResolution: 1.668→1.883 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.641 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1424 / CC1/2: 0.736 / Rpim(I) all: 0.437 / Rrim(I) all: 1.7 / Rsym value: 1.641 / % possible all: 10.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å52.38 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDS20180126data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ryp

4ryp


Resolution: 1.67→27.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 1415 4.97 %RANDOM
Rwork0.2192 ---
obs0.221 28471 63.7 %-
Displacement parametersBiso max: 152.18 Å2 / Biso mean: 48.95 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.1357 Å20 Å20 Å2
2--3.1357 Å20 Å2
3----6.2714 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 1.67→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 15 81 2685
Biso mean--76.27 38.86 -
Num. residues----324
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d929SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes442HARMONIC5
X-RAY DIFFRACTIONt_it2651HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion335SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3265SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2651HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3575HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion17.09
LS refinement shellResolution: 1.67→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2672 28 4.91 %
Rwork0.2455 542 -
all0.2464 570 -
obs--5.92 %
Refinement TLS params.Method: refined / Origin x: 2.6873 Å / Origin y: 11.9323 Å / Origin z: -11.1318 Å
111213212223313233
T0.0507 Å20.0365 Å2-0.1044 Å2--0.2248 Å20.0135 Å2---0.2777 Å2
L0.4444 °20.0695 °2-0.6143 °2-1.6952 °21.8152 °2--5.3463 °2
S-0.1274 Å °0.0493 Å °0.0485 Å °-0.5396 Å °-0.0436 Å °0.2231 Å °-1.0766 Å °-0.3123 Å °0.1711 Å °
Refinement TLS groupSelection details: { A|* }

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