[English] 日本語
Yorodumi
- PDB-7buu: Eucommia ulmoides TPT3, crystal form 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7buu
TitleEucommia ulmoides TPT3, crystal form 1
ComponentsFPS3
KeywordsPLANT PROTEIN / Prenyltransferase / Polyisoprene
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FPS3
B: FPS3


Theoretical massNumber of molelcules
Total (without water)84,3792
Polymers84,3792
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-42 kcal/mol
Surface area30710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.260, 80.260, 278.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
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
11GLUGLUTHRTHR(chain 'A' and (resid 3 through 102 or resid 113 through 348))AA3 - 6519 - 81
12LEULEUMETMET(chain 'A' and (resid 3 through 102 or resid 113 through 348))AA73 - 10289 - 118
13CYSCYSLYSLYS(chain 'A' and (resid 3 through 102 or resid 113 through 348))AA113 - 348129 - 364
24GLUGLUTHRTHR(chain 'B' and (resid 3 through 65 or resid 73 through 348))BB3 - 6519 - 81
25LEULEUMETMET(chain 'B' and (resid 3 through 65 or resid 73 through 348))BB73 - 10289 - 118
26CYSCYSLYSLYS(chain 'B' and (resid 3 through 65 or resid 73 through 348))BB113 - 348129 - 364

-
Components

#1: Protein FPS3


Mass: 42189.465 Da / Num. of mol.: 2
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, DL-Malic acid, Risedronate, MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.44 Å / Num. obs: 19181 / % possible obs: 99.87 % / Redundancy: 28.6 % / Biso Wilson estimate: 85.73 Å2 / CC1/2: 1 / Net I/σ(I): 24.7
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1849 / CC1/2: 0.79

-
Processing

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

4kk2


Resolution: 3→48.44 Å / SU ML: 0.3256 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4676
RfactorNum. reflection% reflection
Rfree0.2329 958 5 %
Rwork0.2223 --
obs0.2228 19167 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 88.31 Å2
Refinement stepCycle: LAST / Resolution: 3→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5482 0 0 0 5482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01135589
X-RAY DIFFRACTIONf_angle_d1.23917560
X-RAY DIFFRACTIONf_chiral_restr0.0674864
X-RAY DIFFRACTIONf_plane_restr0.0073947
X-RAY DIFFRACTIONf_dihedral_angle_d16.7012082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.29541330.34252533X-RAY DIFFRACTION99.89
3.16-3.360.28631330.31542534X-RAY DIFFRACTION99.85
3.36-3.620.27461350.28862545X-RAY DIFFRACTION99.96
3.62-3.980.20921350.22062569X-RAY DIFFRACTION99.96
3.98-4.550.22271360.20782586X-RAY DIFFRACTION100
4.55-5.740.23951390.20272647X-RAY DIFFRACTION100
5.74-48.440.20891470.1882795X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -6.90366700776 Å / Origin y: 3.35993152386 Å / Origin z: -20.5950760074 Å
111213212223313233
T0.337699330672 Å20.0349691278001 Å2-0.0210090925809 Å2-0.669399183144 Å20.034421940195 Å2--0.471133854587 Å2
L1.38572279768 °21.05668701261 °2-0.102639575845 °2-3.43929923327 °20.149604221635 °2--1.20190382016 °2
S0.185278916993 Å °-0.093294743976 Å °0.149655719281 Å °0.447702868094 Å °-0.253729716879 Å °-0.099547555072 Å °-0.0666709581681 Å °0.0999664150232 Å °0.0622184289362 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more