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- PDB-6r05: T. CRUZI FPPS IN COMPLEX WITH N-BENZYL-6-METHYLPYRIDIN-2-AMINE -

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Basic information

Entry
Database: PDB / ID: 6r05
TitleT. CRUZI FPPS IN COMPLEX WITH N-BENZYL-6-METHYLPYRIDIN-2-AMINE
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / farnesyl diphosphate synthase / sterol biosynthesis / farnesyl pyrophosphate / homodimer
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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 6-methyl-~{N}-(phenylmethyl)pyridin-2-amine / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsPetrick, J.K. / Muenzker, L. / Schleberger, C. / Jahnke, W.
Funding support2items
OrganizationGrant numberCountry
Accelerated Early staGe drug dIScovery (AEGIS)765555
European Union675899
CitationJournal: Thesis / Year: 2019
Title: Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery
Authors: Petrick, J.K. / Jahnke, W.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Feb 7, 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 diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9818
Polymers41,3601
Non-polymers6217
Water4,720262
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,96216
Polymers82,7192
Non-polymers1,24314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area8590 Å2
ΔGint-217 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.106, 58.106, 396.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Farnesyl diphosphate synthase


Mass: 41359.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Termini not resolved / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8WS26

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Non-polymers , 6 types, 269 molecules

#2: Chemical ChemComp-JNE / 6-methyl-~{N}-(phenylmethyl)pyridin-2-amine


Mass: 198.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 80 mM MES, 8.5 mM ZnSO4, 19.42% PEG MME 550, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99981 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99981 Å / Relative weight: 1
ReflectionResolution: 1.568→66.115 Å / Num. obs: 57627 / % possible obs: 100 % / Redundancy: 18 % / Biso Wilson estimate: 28.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.024 / Rrim(I) all: 0.102 / Rsym value: 0.099 / Net I/σ(I): 15.1
Reflection shellResolution: 1.568→1.595 Å / Redundancy: 18.3 % / Rmerge(I) obs: 3.102 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2762 / CC1/2: 0.417 / Rpim(I) all: 0.741 / Rrim(I) all: 3.19 / Rsym value: 3.102 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Translation3 Å66.11 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDS20180126data reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWG

4dwg


Resolution: 1.57→22.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2841 4.93 %RANDOM
Rwork0.1832 ---
obs0.185 57590 100 %-
Displacement parametersBiso max: 117.82 Å2 / Biso mean: 35.17 Å2 / Biso min: 17.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.299 Å20 Å20 Å2
2--0.299 Å20 Å2
3----0.5981 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.57→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 34 262 3139
Biso mean--37.66 45.45 -
Num. residues----357
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1011SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes496HARMONIC5
X-RAY DIFFRACTIONt_it2945HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3794SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2945HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3990HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion16.26
LS refinement shellResolution: 1.57→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2005 45 3.91 %
Rwork0.207 1107 -
all0.2068 1152 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: -8.2944 Å / Origin y: -17.7865 Å / Origin z: -20.3451 Å
111213212223313233
T-0.039 Å20.057 Å20.0163 Å2-0.0372 Å20.0045 Å2---0.0857 Å2
L0.7631 °20.0518 °2-0.0292 °2-0.2969 °2-0.0577 °2--0.4978 °2
S0.0214 Å °-0.143 Å °0.1032 Å °0.0388 Å °-0.0134 Å °-0.0159 Å °-0.058 Å °0.015 Å °-0.008 Å °
Refinement TLS groupSelection details: { A|* }

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