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- PDB-6vjc: LmFPPS mutant T164Y in complex with 476A, IPP & Ca -

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Basic information

Entry
Database: PDB / ID: 6vjc
TitleLmFPPS mutant T164Y in complex with 476A, IPP & Ca
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / FPPS / farnesyl diphosphate synthase / Isoprenoid
Function / homology
Function and homology information


dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / 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
3-butyl-1-(2,2-diphosphonoethyl)pyridinium / ACETATE ION / ISOPENTYL PYROPHOSPHATE / DI(HYDROXYETHYL)ETHER / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsMaheshwari, S. / Kim, Y.S. / Aripirala, S. / Gabelli, S.B.
CitationJournal: Biochemistry / Year: 2020
Title: Identifying Structural Determinants of Product Specificity in Leishmania major Farnesyl Diphosphate Synthase.
Authors: Maheshwari, S. / Kim, Y.S. / Aripirala, S. / Murphy, M. / Amzel, L.M. / Gabelli, S.B.
History
DepositionJan 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,82415
Polymers82,2152
Non-polymers1,60913
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-94 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.525, 85.889, 107.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Farnesyl pyrophosphate synthase


Mass: 41107.273 Da / Num. of mol.: 2 / Mutation: T164Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: FPPS, LMJF_22_1360 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4QBL1, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 6 types, 711 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IPR / ISOPENTYL PYROPHOSPHATE


Mass: 248.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-476 / 3-butyl-1-(2,2-diphosphonoethyl)pyridinium


Mass: 324.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20NO6P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 698 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 100 mM MES, 15-25 % PEG 8000, 100-200 mM CaAcetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 67996 / % possible obs: 97.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.081 / Χ2: 1.618 / Net I/σ(I): 10.5 / Num. measured all: 422649
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.862.60.68854901.627179.4
1.86-1.943.20.39565441.123195.5
1.94-2.035.20.25869040.8931100
2.03-2.137.10.19768921.0461100
2.13-2.277.10.15669351.2071100
2.27-2.447.20.12569351.4261100
2.44-2.697.20.10469651.5691100
2.69-3.087.30.08369701.8821100
3.08-3.887.20.06570532.3121100
3.88-5070.05673082.488199.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JZX

4jzx


Resolution: 1.8→42.98 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1812 / WRfactor Rwork: 0.1423 / FOM work R set: 0.8327 / SU B: 2.598 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1219 / SU Rfree: 0.1179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 3433 5.1 %RANDOM
Rwork0.1583 ---
obs0.1603 64413 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.1 Å2 / Biso mean: 23.617 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å20 Å2
2---0.71 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 1.8→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 89 698 6549
Biso mean--23.24 33.61 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136024
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175592
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.658174
X-RAY DIFFRACTIONr_angle_other_deg1.5851.58112952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58723.113302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.011151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4641526
X-RAY DIFFRACTIONr_chiral_restr0.1330.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026702
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021256
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 199 -
Rwork0.499 3716 -
all-3915 -
obs--76.86 %

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