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- PDB-7buw: Eucommia ulmoides TPT3 mutant -C94Y/A95F -

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Basic information

Entry
Database: PDB / ID: 7buw
TitleEucommia ulmoides TPT3 mutant -C94Y/A95F
ComponentsFPS3
KeywordsPLANT PROTEIN / Prenyltransferase / Polyisoprene
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / 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
Biological speciesEucommia ulmoides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKajiura, H. / Yoshizawa, T. / Tokumoto, Y. / Suzuki, N. / Takeno, S. / Takeno, K.J. / Yamashita, T. / Tanaka, S. / Kaneko, Y. / Fujiyama, K. ...Kajiura, H. / Yoshizawa, T. / Tokumoto, Y. / Suzuki, N. / Takeno, S. / Takeno, K.J. / Yamashita, T. / Tanaka, S. / Kaneko, Y. / Fujiyama, K. / Matsumura, H. / Nakazawa, Y.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05732 Japan
Japan Society for the Promotion of Science (JSPS)18K06094 Japan
Japan Society for the Promotion of Science (JSPS)19H04735 Japan
Japan Society for the Promotion of Science (JSPS)19K16060 Japan
CitationJournal: Commun Biol / Year: 2021
Title: Structure-function studies of ultrahigh molecular weight isoprenes provide key insights into their biosynthesis.
Authors: Kajiura, H. / Yoshizawa, T. / Tokumoto, Y. / Suzuki, N. / Takeno, S. / Takeno, K.J. / Yamashita, T. / Tanaka, S.I. / Kaneko, Y. / Fujiyama, K. / Matsumura, H. / Nakazawa, Y.
History
DepositionApr 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FPS3
B: FPS3


Theoretical massNumber of molelcules
Total (without water)83,8922
Polymers83,8922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-35 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.253, 84.253, 181.189
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain 'A' and (resid 6 through 24 or resid 26...AA6 - 2322 - 39
12GLYGLYARGARG(chain 'A' and (resid 6 through 24 or resid 26...AA26 - 6242 - 78
13SERSERASPASP(chain 'A' and (resid 6 through 24 or resid 26...AA74 - 10388 - 117
14ILEILEGLUGLU(chain 'A' and (resid 6 through 24 or resid 26...AA123 - 178137 - 192
15ASNASNPHEPHE(chain 'A' and (resid 6 through 24 or resid 26...AA180 - 244194 - 258
16CYSCYSLEULEU(chain 'A' and (resid 6 through 24 or resid 26...AA262 - 281276 - 295
17ASPASPARGARG(chain 'A' and (resid 6 through 24 or resid 26...AA283 - 287297 - 301
18ASPASPARGARG(chain 'A' and (resid 6 through 24 or resid 26...AA289 - 346303 - 360
29SERSERSERSER(chain 'B' and (resid 6 through 24 or resid 26...BB6 - 2322 - 39
210GLYGLYARGARG(chain 'B' and (resid 6 through 24 or resid 26...BB26 - 6242 - 78
211SERSERASPASP(chain 'B' and (resid 6 through 24 or resid 26...BB74 - 10388 - 117
212ILEILEGLUGLU(chain 'B' and (resid 6 through 24 or resid 26...BB123 - 178137 - 192
213ASNASNPHEPHE(chain 'B' and (resid 6 through 24 or resid 26...BB180 - 244194 - 258
214CYSCYSLEULEU(chain 'B' and (resid 6 through 24 or resid 26...BB262 - 281276 - 295
215ASPASPARGARG(chain 'B' and (resid 6 through 24 or resid 26...BB283 - 287297 - 301
216ASPASPARGARG(chain 'B' and (resid 6 through 24 or resid 26...BB289 - 346303 - 360

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Components

#1: Protein FPS3


Mass: 41946.160 Da / Num. of mol.: 2 / Mutation: replaced NSKY(66-69) with GG, C94Y, A95F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eucommia ulmoides (plant) / Gene: FPS3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L3KPU1

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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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: CHES, PEG 8000, Risedronate, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→46.53 Å / Num. obs: 11760 / % possible obs: 99.9 % / Redundancy: 21.1 % / Biso Wilson estimate: 69.26 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.2
Reflection shellResolution: 3.3→3.418 Å / Num. unique obs: 1137 / CC1/2: 0.783

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KK2

4kk2


Resolution: 3.3→46.53 Å / SU ML: 0.497 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.7627
RfactorNum. reflection% reflection
Rfree0.3104 588 5 %
Rwork0.2527 --
obs0.2556 11754 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.42 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 0 0 5108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415202
X-RAY DIFFRACTIONf_angle_d0.7777032
X-RAY DIFFRACTIONf_chiral_restr0.0446806
X-RAY DIFFRACTIONf_plane_restr0.0056880
X-RAY DIFFRACTIONf_dihedral_angle_d19.56821924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.630.38041430.3052730X-RAY DIFFRACTION99.97
3.63-4.160.32761450.25752753X-RAY DIFFRACTION100
4.16-5.240.30251460.23672770X-RAY DIFFRACTION99.86
5.24-46.530.27561540.24022913X-RAY DIFFRACTION100

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