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- PDB-6ww1: Crystal structure of the LmFPPS mutant E97Y -

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Basic information

Entry
Database: PDB / ID: 6ww1
TitleCrystal structure of the LmFPPS mutant E97Y
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / FPPS / Farnesyl diphosphate synthase
Function / homology
Function and homology information


dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase 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 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsMaheshwari, S. / Kim, Y.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
DepositionMay 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,60614
Polymers82,1032
Non-polymers1,50312
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-97 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.699, 86.078, 107.425
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: 41051.254 Da / Num. of mol.: 2 / Mutation: E97Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: FPPS, LMJF_22_1360 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4QBL1, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 5 types, 607 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.87 % / Mosaicity: 0.812 °
Crystal growTemperature: 291.5 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 FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→67.17 Å / Num. obs: 43443 / % possible obs: 90.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Χ2: 1.735 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.05-2.092.70.24118520.887178.7
2.09-2.122.70.21518830.849179.4
2.12-2.162.80.21219090.762180.8
2.16-2.212.60.41618950.904180.2
2.21-2.262.80.13519552.126183.2
2.26-2.312.90.21419611.781182.8
2.31-2.373.40.20420331.256185.9
2.37-2.433.70.14420971.415188.7
2.43-2.540.13321311.546189.4
2.5-2.584.20.12721611.513190.8
2.58-2.684.30.12121681.626191.7
2.68-2.784.50.11822371.681193.8
2.78-2.914.80.10722891.907195.1
2.91-3.065.10.09423071.96196.9
3.06-3.255.70.08823362.075197.4
3.25-3.516.80.08623771.973198.7
3.51-3.866.70.09924013.926198.8
3.86-4.427.10.05224091.479199.3
4.42-5.567.20.04124661.13199.5
2.05-2.096.80.03525761.104199

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JZX

4jzx


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.691 / SU ML: 0.153 / SU R Cruickshank DPI: 0.3075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 2161 5.1 %RANDOM
Rwork0.2126 ---
obs0.2168 40295 89.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.29 Å2 / Biso mean: 18.426 Å2 / Biso min: 5.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0 Å2
2---0.94 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 82 595 6431
Biso mean--14.51 24.59 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025962
X-RAY DIFFRACTIONr_bond_other_d0.0040.026
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9618086
X-RAY DIFFRACTIONr_angle_other_deg1.042312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4215724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18224.318264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.423151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4221526
X-RAY DIFFRACTIONr_chiral_restr0.1150.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024426
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 135 -
Rwork0.184 2500 -
all-2635 -
obs--78.52 %

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