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- PDB-6w7i: LmFPPS mutant T164W in complex with 476A, IPP & Ca -

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Basic information

Entry
Database: PDB / ID: 6w7i
TitleLmFPPS mutant T164W 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 / 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 / DI(HYDROXYETHYL)ETHER / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsMaheshwari, S. / Kim, Y.S. / Aripirala, S. / Gabelli, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
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
DepositionMar 19, 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)83,81114
Polymers82,2612
Non-polymers1,55012
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-87 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.932, 79.977, 81.175
Angle α, β, γ (deg.)90.000, 106.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Farnesyl pyrophosphate synthase


Mass: 41130.309 Da / Num. of mol.: 2 / Mutation: T164W
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, 452 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IPR / ISOPENTYL PYROPHOSPHATE


Mass: 248.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14O7P2
#5: 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
#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.: 440 / 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: 2.23 Å3/Da / Density % sol: 44.91 % / Mosaicity: 0.882 °
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 RAXIS IV / Detector: IMAGE PLATE / 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: 2.1→77.85 Å / Num. obs: 38828 / % possible obs: 92.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.072 / Χ2: 2.637 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.181.90.21724042.325157.8
2.18-2.262.10.18331242.397173.6
2.26-2.372.60.16238712.423192.7
2.37-2.493.20.14541472.505199.1
2.49-2.653.50.12941662.596199.3
2.65-2.853.50.10941882.661199.5
2.85-3.143.50.08642012.749199.7
3.14-3.593.60.06442122.852199.9
3.59-4.523.60.05242662.824199.9
4.52-503.50.04842492.506198.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JZX

4jzx


Resolution: 2.1→77.85 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.826 / SU ML: 0.132 / SU R Cruickshank DPI: 0.3033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.218 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1953 5 %RANDOM
Rwork0.1841 ---
obs0.1868 36846 91.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 106.3 Å2 / Biso mean: 19.64 Å2 / Biso min: 5.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.32 Å2
2---0.16 Å20 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 2.1→77.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5766 0 88 440 6294
Biso mean--15.9 27.77 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226050
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9598221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9155744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06324.489274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.997151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6831526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024524
X-RAY DIFFRACTIONr_nbd_refined0.2010.23399
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2487
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.217
LS refinement shellResolution: 2.102→2.157 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 79 -
Rwork0.215 1625 -
all-1704 -
obs--54.91 %

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