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- PDB-7buv: Eucommia ulmoides TPT3, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 7buv
TitleEucommia ulmoides TPT3, crystal form 2
ComponentsFPS3
KeywordsPLANT PROTEIN / Prenyltransferase / Polyisoprene
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / metal ion binding
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
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
C: FPS3
D: FPS3
E: FPS3
F: FPS3
G: FPS3


Theoretical massNumber of molelcules
Total (without water)295,3267
Polymers295,3267
Non-polymers00
Water0
1
A: FPS3
B: FPS3


Theoretical massNumber of molelcules
Total (without water)84,3792
Polymers84,3792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-42 kcal/mol
Surface area32800 Å2
MethodPISA
2
C: FPS3
D: FPS3


Theoretical massNumber of molelcules
Total (without water)84,3792
Polymers84,3792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-38 kcal/mol
Surface area31620 Å2
MethodPISA
3
E: FPS3
F: FPS3


Theoretical massNumber of molelcules
Total (without water)84,3792
Polymers84,3792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-41 kcal/mol
Surface area32450 Å2
MethodPISA
4
G: FPS3

G: FPS3


Theoretical massNumber of molelcules
Total (without water)84,3792
Polymers84,3792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3490 Å2
ΔGint-42 kcal/mol
Surface area31900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.386, 131.060, 103.924
Angle α, β, γ (deg.)90.000, 111.980, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

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
11SERSERLEULEU(chain 'A' and (resid 6 through 20 or resid 28...AA6 - 2022 - 36
12THRTHRPROPRO(chain 'A' and (resid 6 through 20 or resid 28...AA28 - 4444 - 60
13LYSLYSGLUGLU(chain 'A' and (resid 6 through 20 or resid 28...AA47 - 6363 - 79
14SERSERMETMET(chain 'A' and (resid 6 through 20 or resid 28...AA74 - 10290 - 118
15PHEPHELEULEU(chain 'A' and (resid 6 through 20 or resid 28...AA115 - 213131 - 229
16LEULEUASPASP(chain 'A' and (resid 6 through 20 or resid 28...AA217 - 242233 - 258
17ASPASPILEILE(chain 'A' and (resid 6 through 20 or resid 28...AA246 - 250262 - 266
18ILEILEASPASP(chain 'A' and (resid 6 through 20 or resid 28...AA253 - 283269 - 299
19PROPROTHRTHR(chain 'A' and (resid 6 through 20 or resid 28...AA290 - 302306 - 318
110GLUGLULEULEU(chain 'A' and (resid 6 through 20 or resid 28...AA306 - 327322 - 343
111ASNASNARGARG(chain 'A' and (resid 6 through 20 or resid 28...AA329 - 346345 - 362
212SERSERLEULEU(chain 'B' and (resid 6 through 20 or resid 28...BB6 - 2022 - 36
213THRTHRPROPRO(chain 'B' and (resid 6 through 20 or resid 28...BB28 - 4444 - 60
214LYSLYSGLUGLU(chain 'B' and (resid 6 through 20 or resid 28...BB47 - 6363 - 79
215SERSERMETMET(chain 'B' and (resid 6 through 20 or resid 28...BB74 - 10290 - 118
216PHEPHELEULEU(chain 'B' and (resid 6 through 20 or resid 28...BB115 - 213131 - 229
217LEULEUASPASP(chain 'B' and (resid 6 through 20 or resid 28...BB217 - 242233 - 258
218ASPASPILEILE(chain 'B' and (resid 6 through 20 or resid 28...BB246 - 250262 - 266
219ILEILEASPASP(chain 'B' and (resid 6 through 20 or resid 28...BB253 - 283269 - 299
220PROPROTHRTHR(chain 'B' and (resid 6 through 20 or resid 28...BB290 - 302306 - 318
221GLUGLULEULEU(chain 'B' and (resid 6 through 20 or resid 28...BB306 - 327322 - 343
222ASNASNARGARG(chain 'B' and (resid 6 through 20 or resid 28...BB329 - 346345 - 362
323SERSERLEULEU(chain 'C' and (resid 6 through 20 or resid 28...CC6 - 2022 - 36
324THRTHRPROPRO(chain 'C' and (resid 6 through 20 or resid 28...CC28 - 4444 - 60
325LYSLYSGLUGLU(chain 'C' and (resid 6 through 20 or resid 28...CC47 - 6363 - 79
326SERSERMETMET(chain 'C' and (resid 6 through 20 or resid 28...CC74 - 10290 - 118
327PHEPHELEULEU(chain 'C' and (resid 6 through 20 or resid 28...CC115 - 213131 - 229
328LEULEUASPASP(chain 'C' and (resid 6 through 20 or resid 28...CC217 - 242233 - 258
329ASPASPILEILE(chain 'C' and (resid 6 through 20 or resid 28...CC246 - 250262 - 266
330ILEILEASPASP(chain 'C' and (resid 6 through 20 or resid 28...CC253 - 283269 - 299
331PROPROTHRTHR(chain 'C' and (resid 6 through 20 or resid 28...CC290 - 302306 - 318
332GLUGLULEULEU(chain 'C' and (resid 6 through 20 or resid 28...CC306 - 327322 - 343
333ASNASNARGARG(chain 'C' and (resid 6 through 20 or resid 28...CC329 - 346345 - 362
434SERSERLEULEU(chain 'D' and (resid 6 through 20 or resid 28...DD6 - 2022 - 36
435THRTHRPROPRO(chain 'D' and (resid 6 through 20 or resid 28...DD28 - 4444 - 60
436LYSLYSGLUGLU(chain 'D' and (resid 6 through 20 or resid 28...DD47 - 6363 - 79
437SERSERMETMET(chain 'D' and (resid 6 through 20 or resid 28...DD74 - 10290 - 118
438PHEPHELEULEU(chain 'D' and (resid 6 through 20 or resid 28...DD115 - 213131 - 229
439LEULEUASPASP(chain 'D' and (resid 6 through 20 or resid 28...DD217 - 242233 - 258
440ASPASPILEILE(chain 'D' and (resid 6 through 20 or resid 28...DD246 - 250262 - 266
441ILEILEASPASP(chain 'D' and (resid 6 through 20 or resid 28...DD253 - 283269 - 299
442PROPROTHRTHR(chain 'D' and (resid 6 through 20 or resid 28...DD290 - 302306 - 318
443GLUGLULEULEU(chain 'D' and (resid 6 through 20 or resid 28...DD306 - 327322 - 343
444ASNASNARGARG(chain 'D' and (resid 6 through 20 or resid 28...DD329 - 346345 - 362
545SERSERLEULEU(chain 'E' and (resid 6 through 20 or resid 28...EE6 - 2022 - 36
546THRTHRPROPRO(chain 'E' and (resid 6 through 20 or resid 28...EE28 - 4444 - 60
547LYSLYSGLUGLU(chain 'E' and (resid 6 through 20 or resid 28...EE47 - 6363 - 79
548SERSERMETMET(chain 'E' and (resid 6 through 20 or resid 28...EE74 - 10290 - 118
549PHEPHELEULEU(chain 'E' and (resid 6 through 20 or resid 28...EE115 - 213131 - 229
550LEULEUASPASP(chain 'E' and (resid 6 through 20 or resid 28...EE217 - 242233 - 258
551ASPASPILEILE(chain 'E' and (resid 6 through 20 or resid 28...EE246 - 250262 - 266
552ILEILEASPASP(chain 'E' and (resid 6 through 20 or resid 28...EE253 - 283269 - 299
553PROPROTHRTHR(chain 'E' and (resid 6 through 20 or resid 28...EE290 - 302306 - 318
554GLUGLULEULEU(chain 'E' and (resid 6 through 20 or resid 28...EE306 - 327322 - 343
555ASNASNARGARG(chain 'E' and (resid 6 through 20 or resid 28...EE329 - 346345 - 362
656SERSERLEULEU(chain 'F' and (resid 6 through 20 or resid 28...FF6 - 2022 - 36
657THRTHRPROPRO(chain 'F' and (resid 6 through 20 or resid 28...FF28 - 4444 - 60
658LYSLYSGLUGLU(chain 'F' and (resid 6 through 20 or resid 28...FF47 - 6363 - 79
659SERSERMETMET(chain 'F' and (resid 6 through 20 or resid 28...FF74 - 10290 - 118
660PHEPHELEULEU(chain 'F' and (resid 6 through 20 or resid 28...FF115 - 213131 - 229
661LEULEUASPASP(chain 'F' and (resid 6 through 20 or resid 28...FF217 - 242233 - 258
662ASPASPILEILE(chain 'F' and (resid 6 through 20 or resid 28...FF246 - 250262 - 266
663ILEILEASPASP(chain 'F' and (resid 6 through 20 or resid 28...FF253 - 283269 - 299
664PROPROTHRTHR(chain 'F' and (resid 6 through 20 or resid 28...FF290 - 302306 - 318
665GLUGLULEULEU(chain 'F' and (resid 6 through 20 or resid 28...FF306 - 327322 - 343
666ASNASNARGARG(chain 'F' and (resid 6 through 20 or resid 28...FF329 - 346345 - 362
767SERSERLEULEU(chain 'G' and (resid 6 through 20 or resid 28...GG6 - 2022 - 36
768THRTHRPROPRO(chain 'G' and (resid 6 through 20 or resid 28...GG28 - 4444 - 60
769LYSLYSGLUGLU(chain 'G' and (resid 6 through 20 or resid 28...GG47 - 6363 - 79
770SERSERMETMET(chain 'G' and (resid 6 through 20 or resid 28...GG74 - 10290 - 118
771PHEPHELEULEU(chain 'G' and (resid 6 through 20 or resid 28...GG115 - 213131 - 229
772LEULEUASPASP(chain 'G' and (resid 6 through 20 or resid 28...GG217 - 242233 - 258
773ASPASPILEILE(chain 'G' and (resid 6 through 20 or resid 28...GG246 - 250262 - 266
774ILEILEASPASP(chain 'G' and (resid 6 through 20 or resid 28...GG253 - 283269 - 299
775PROPROTHRTHR(chain 'G' and (resid 6 through 20 or resid 28...GG290 - 302306 - 318
776GLUGLULEULEU(chain 'G' and (resid 6 through 20 or resid 28...GG306 - 327322 - 343
777ASNASNARGARG(chain 'G' and (resid 6 through 20 or resid 28...GG329 - 346345 - 362

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Components

#1: Protein
FPS3


Mass: 42189.465 Da / Num. of mol.: 7
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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, DL-Malic acid, Risedronate, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→48.19 Å / Num. obs: 43925 / % possible obs: 99.82 % / Redundancy: 5.8 % / Biso Wilson estimate: 116.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.96
Reflection shellResolution: 3.3→3.418 Å / Num. unique obs: 4399 / CC1/2: 0.66

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Processing

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

4kk2


Resolution: 3.3→48.19 Å / SU ML: 0.725 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.9623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3043 2193 5 %
Rwork0.2816 41706 -
obs0.2828 43899 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.82 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18385 0 0 0 18385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003718724
X-RAY DIFFRACTIONf_angle_d0.785425310
X-RAY DIFFRACTIONf_chiral_restr0.04352916
X-RAY DIFFRACTIONf_plane_restr0.00413149
X-RAY DIFFRACTIONf_dihedral_angle_d13.5066944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.370.49381380.40112613X-RAY DIFFRACTION99.93
3.37-3.450.38171370.3922609X-RAY DIFFRACTION100
3.45-3.540.45281360.39922575X-RAY DIFFRACTION100
3.54-3.630.41211380.36832615X-RAY DIFFRACTION99.96
3.63-3.740.38311350.35522577X-RAY DIFFRACTION100
3.74-3.860.35991370.33722600X-RAY DIFFRACTION100
3.86-40.30441370.33272597X-RAY DIFFRACTION99.96
4-4.160.36281370.32752618X-RAY DIFFRACTION99.93
4.16-4.350.35871370.30722590X-RAY DIFFRACTION99.93
4.35-4.580.31811350.28132577X-RAY DIFFRACTION100
4.58-4.860.31091390.27252626X-RAY DIFFRACTION99.96
4.86-5.240.27721370.28542608X-RAY DIFFRACTION99.96
5.24-5.760.37131370.30692614X-RAY DIFFRACTION100
5.76-6.60.31291380.31662617X-RAY DIFFRACTION100
6.6-8.30.24781390.23772635X-RAY DIFFRACTION100
8.3-48.190.19671360.18752635X-RAY DIFFRACTION98.19

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