[English] 日本語
Yorodumi
- PDB-6j1n: Anisodus acutangulus type III polyketide sythase AaPKS2 in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j1n
TitleAnisodus acutangulus type III polyketide sythase AaPKS2 in complex with 4-carboxy-3-oxobutanoyl-CoA
ComponentsA. acutangulus PKS2
KeywordsBIOSYNTHETIC PROTEIN / Anisodus acutangulus / type III polyketide sythase / tropane alkaloids biosynthesis
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Chem-B7X
Function and homology information
Biological speciesAnisodus acutangulus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.532 Å
AuthorsFang, C.L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31822001 China
CitationJournal: Nat Commun / Year: 2019
Title: Tropane alkaloids biosynthesis involves an unusual type III polyketide synthase and non-enzymatic condensation.
Authors: Huang, J.P. / Fang, C. / Ma, X. / Wang, L. / Yang, J. / Luo, J. / Yan, Y. / Zhang, Y. / Huang, S.X.
History
DepositionDec 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: A. acutangulus PKS2
B: A. acutangulus PKS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2454
Polymers93,4542
Non-polymers1,7912
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-9 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.347, 108.347, 191.485
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein A. acutangulus PKS2


Mass: 46726.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anisodus acutangulus (plant) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
#2: Chemical ChemComp-B7X / (3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,19,21-tetraoxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide (non-preferred name)


Mass: 895.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H40N7O20P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 3.47 Å3/Da / Density % sol: 64.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1% tryptone, 0.05M HEPES 7.0, 20% PEG3350, 0.001M Sodium azide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 44048 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 16.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.024 / Rrim(I) all: 0.095 / Rsym value: 0.092 / Χ2: 0.96 / Net I/σ(I): 34.1
Reflection shellResolution: 2.53→2.57 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.472 / Num. unique obs: 2176 / CC1/2: 0.974 / Rpim(I) all: 0.122 / Rrim(I) all: 0.488 / Rsym value: 0.472 / Χ2: 0.921 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CML

1cml


Resolution: 2.532→47.149 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1911 2009 4.57 %
Rwork0.1655 41988 -
obs0.1666 43997 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.75 Å2 / Biso mean: 33.6874 Å2 / Biso min: 15.13 Å2
Refinement stepCycle: final / Resolution: 2.532→47.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5778 0 114 404 6296
Biso mean--63.94 38.57 -
Num. residues----755
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5323-2.59560.25541400.21429143054
2.5956-2.66580.23851440.194229453089
2.6658-2.74430.26041450.18829753120
2.7443-2.83280.20131390.180829763115
2.8328-2.93410.21881450.177929743119
2.9341-3.05150.20831380.187529643102
3.0515-3.19040.20081430.185530003143
3.1904-3.35850.19871420.179829603102
3.3585-3.56890.20281440.170429723116
3.5689-3.84430.1981440.162329953139
3.8443-4.2310.17071440.151730203164
4.231-4.84270.15321470.129430133160
4.8427-6.09920.17921430.150430823225
6.0992-47.15730.15921510.159731983349

+
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://pdbjlvh1.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