[English] 日本語
Yorodumi
- PDB-8wu6: Structure of a Nerylneryl Diphosphate Synthase from Solanum lycop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wu6
TitleStructure of a Nerylneryl Diphosphate Synthase from Solanum lycopersicum
ComponentsNerylneryl diphosphate synthase CPT2, chloroplastic
KeywordsBIOSYNTHETIC PROTEIN / cis-prenyltransferase
Function / homology
Function and homology information


nerylneryl diphosphate synthase / dimethylallylcistransferase activity / plastid membrane organization / polyprenol biosynthetic process / prenyltransferase activity / chloroplast stroma / response to cold / chloroplast / magnesium ion binding
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
Nerylneryl diphosphate synthase CPT2, chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsLi, F.R. / Wang, Q.L. / Pan, X.M. / Dong, L.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073746 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase.
Authors: Li, F.R. / Wang, Q. / Pan, X. / Xu, H.M. / Dong, L.B.
History
DepositionOct 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nerylneryl diphosphate synthase CPT2, chloroplastic
B: Nerylneryl diphosphate synthase CPT2, chloroplastic


Theoretical massNumber of molelcules
Total (without water)73,7932
Polymers73,7932
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This protein appears a homodimer in our gel filtration column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.370, 125.370, 52.990
Angle α, β, γ (deg.)90.00, 110.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nerylneryl diphosphate synthase CPT2, chloroplastic


Mass: 36896.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: CPT2 / Organ: Plant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7WQ45
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.33 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1M BICINE (pH 7.6), 30% v/v PEG monomethyl ether 550, 0.1 M Sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.81→62.68 Å / Num. obs: 46804 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.8
Reflection shellResolution: 1.81→1.91 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 8.1 / Num. unique obs: 6864 / CC1/2: 0.98

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1-4487)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTv4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→28.16 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 2012 4.3 %
Rwork0.1759 --
obs0.1772 46756 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 0 351 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.959
X-RAY DIFFRACTIONf_dihedral_angle_d6.127481
X-RAY DIFFRACTIONf_chiral_restr0.152556
X-RAY DIFFRACTIONf_plane_restr0.012643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.23071580.193186X-RAY DIFFRACTION100
1.86-1.910.20981300.17113225X-RAY DIFFRACTION100
1.91-1.960.19081580.1683209X-RAY DIFFRACTION100
1.96-2.020.19451290.17293247X-RAY DIFFRACTION100
2.02-2.10.23331580.17373172X-RAY DIFFRACTION100
2.1-2.180.20581370.17353233X-RAY DIFFRACTION100
2.18-2.280.2381450.17183219X-RAY DIFFRACTION100
2.28-2.40.23911460.18093222X-RAY DIFFRACTION100
2.4-2.550.22541500.18153213X-RAY DIFFRACTION100
2.55-2.750.23341410.1883229X-RAY DIFFRACTION100
2.75-3.020.21951470.19053244X-RAY DIFFRACTION100
3.02-3.460.19151430.18393227X-RAY DIFFRACTION100
3.46-4.360.19091400.15513211X-RAY DIFFRACTION99
4.36-28.160.17281300.17752907X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: 11.5374 Å / Origin y: 14.3119 Å / Origin z: 11.9537 Å
111213212223313233
T0.0823 Å20.0061 Å20.0011 Å2-0.1137 Å20.0053 Å2--0.0884 Å2
L0.4355 °2-0.0754 °2-0.0055 °2-1.1307 °2-0.1784 °2--0.4073 °2
S0.021 Å °-0.0325 Å °-0.0035 Å °-0.1403 Å °-0.0372 Å °0.0109 Å °0.021 Å °-0.007 Å °-0.005 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