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- PDB-8wd5: Crystal structure of farnesyl diphosphate synthase FPPS1 from sil... -

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Basic information

Entry
Database: PDB / ID: 8wd5
TitleCrystal structure of farnesyl diphosphate synthase FPPS1 from silkworm, Bombyx mori
ComponentsFarnesyl pyrophosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / mevalonate pathway / JH biosynthesis / terpenoids production / Lepidopteran FPPS
Function / homology
Function and homology information


pheromone biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGuo, P.C. / Fang, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970468 China
National Natural Science Foundation of China (NSFC)32370517 China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structural Insights into the Substrate Binding of Farnesyl Diphosphate Synthase FPPS1 from Silkworm, Bombyx mori.
Authors: Fang, H. / Zheng, H. / Yang, Y. / Hu, Y. / Wang, Z. / Xia, Q. / Guo, P.
History
DepositionSep 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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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)85,2324
Polymers85,0482
Non-polymers1842
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.530, 64.967, 108.378
Angle α, β, γ (deg.)90.000, 92.425, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 42523.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence is corresponding to the entry of BMSK0011099 in the SilkDB 3.0 (https://silkdb.bioinfotoolkits.net/main/species-info/-1)
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmFPS, 692433 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q95P28
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% Tacsimate pH 5.0, 0.1 M sodium citrate, pH 5.6, 16% polyethylene glycol 3350
Temp details: 16

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→45.4 Å / Num. obs: 21918 / % possible obs: 99.6 % / Redundancy: 4.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.069 / Rrim(I) all: 0.15 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.476 / Num. unique obs: 3180 / CC1/2: 0.837 / Rpim(I) all: 0.253 / Rrim(I) all: 0.542 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→42.365 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.84 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.229 / Average fsc free: 0.8594 / Average fsc work: 0.8825 / Cross valid method: FREE R-VALUE / ESU R Free: 0.428
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2923 1026 4.685 %
Rwork0.2398 20872 -
all0.242 --
obs-21898 99.491 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.376 Å2
Baniso -1Baniso -2Baniso -3
1-1.073 Å2-0 Å2-2.425 Å2
2--0.798 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 12 7 5513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0125634
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6427606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8223.243296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.445151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8261528
X-RAY DIFFRACTIONr_chiral_restr0.0720.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024204
X-RAY DIFFRACTIONr_nbd_refined0.2220.22526
X-RAY DIFFRACTIONr_nbtor_refined0.2930.23823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0720.21
X-RAY DIFFRACTIONr_mcbond_it2.0873.8352695
X-RAY DIFFRACTIONr_mcangle_it3.3525.7423360
X-RAY DIFFRACTIONr_scbond_it2.5944.1762939
X-RAY DIFFRACTIONr_scangle_it4.2496.1414246
X-RAY DIFFRACTIONr_lrange_it6.73152.2538360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.335640.2781550X-RAY DIFFRACTION99.9381
2.873-2.9510.33930.2851466X-RAY DIFFRACTION99.8719
2.951-3.0370.323810.2691472X-RAY DIFFRACTION99.7431
3.037-3.130.338530.2731406X-RAY DIFFRACTION100
3.13-3.2330.289720.2751380X-RAY DIFFRACTION99.9312
3.233-3.3460.269550.2581340X-RAY DIFFRACTION99.9284
3.346-3.4720.319780.2251254X-RAY DIFFRACTION99.7006
3.472-3.6140.305700.2311230X-RAY DIFFRACTION99.8464
3.614-3.7750.228650.2241180X-RAY DIFFRACTION99.6797
3.775-3.9590.264480.2221145X-RAY DIFFRACTION99.5826
3.959-4.1720.28280.2271082X-RAY DIFFRACTION98.7544
4.172-4.4250.311370.2061007X-RAY DIFFRACTION98.6768
4.425-4.730.226330.203983X-RAY DIFFRACTION98.6408
4.73-5.1080.322560.237892X-RAY DIFFRACTION99.4753
5.108-5.5950.373510.254806X-RAY DIFFRACTION99.1898
5.595-6.2530.356380.294759X-RAY DIFFRACTION99.8747
6.253-7.2160.284280.249683X-RAY DIFFRACTION99.5798
7.216-8.8280.2350.212553X-RAY DIFFRACTION100
8.828-12.4440.239360.188437X-RAY DIFFRACTION99.3697
12.444-42.3650.42450.309247X-RAY DIFFRACTION90.9747

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