[English] 日本語
Yorodumi
- PDB-7dtq: Apo Crystal Structure of Octaketide Synthase from A. arborescens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dtq
TitleApo Crystal Structure of Octaketide Synthase from A. arborescens
ComponentsOctaketide synthase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


flavonoid biosynthetic process / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / protein homodimerization activity
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Octaketide synthase 1
Similarity search - Component
Biological speciesAloe arborescens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLi, T.L. / Adhikari, K. / Li, Y.S.
CitationJournal: To Be Published
Title: Apo Crystal Structure of Octaketide synthase from Aloe arborescens.
Authors: Li, T.L. / Adhikari, K. / Li, Y.S.
History
DepositionJan 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Octaketide synthase 1
B: Octaketide synthase 1
C: Octaketide synthase 1
D: Octaketide synthase 1


Theoretical massNumber of molelcules
Total (without water)178,4894
Polymers178,4894
Non-polymers00
Water00
1
A: Octaketide synthase 1
B: Octaketide synthase 1


Theoretical massNumber of molelcules
Total (without water)89,2452
Polymers89,2452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-10 kcal/mol
Surface area25770 Å2
MethodPISA
2
C: Octaketide synthase 1

D: Octaketide synthase 1


Theoretical massNumber of molelcules
Total (without water)89,2452
Polymers89,2452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Buried area6030 Å2
ΔGint-9 kcal/mol
Surface area25690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.901, 51.679, 131.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Octaketide synthase 1 / OKS


Mass: 44622.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aloe arborescens (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q3L7F5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium potassium tartarate, 0.1M Bistris propane (pH 6.5) 20% PEG 3350

-
Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→25.6 Å / Num. obs: 171608 / % possible obs: 95.31 % / Redundancy: 3.1 % / CC1/2: 0.85 / Net I/σ(I): 2.11
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 171608 / CC1/2: 0.85

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D3M

2d3m


Resolution: 1.75→25.6 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 2011 1.17 %
Rwork0.2251 --
obs0.2253 171608 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12096 0 0 0 12096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812364
X-RAY DIFFRACTIONf_angle_d1.08716748
X-RAY DIFFRACTIONf_dihedral_angle_d4.8717444
X-RAY DIFFRACTIONf_chiral_restr0.0781852
X-RAY DIFFRACTIONf_plane_restr0.0072176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.26391340.261611391X-RAY DIFFRACTION90
1.7938-1.810.18741570.166513043X-RAY DIFFRACTION99
1.81-1.84220.23151430.231511970X-RAY DIFFRACTION95
1.8422-1.89640.27761360.251611807X-RAY DIFFRACTION94
1.8964-1.95760.25181380.241611839X-RAY DIFFRACTION94
1.9576-2.02760.27541360.246411770X-RAY DIFFRACTION93
2.0276-2.10870.3121470.247111770X-RAY DIFFRACTION93
2.1087-2.20460.25661420.251111847X-RAY DIFFRACTION94
2.2046-2.32080.28171470.254912042X-RAY DIFFRACTION95
2.3208-2.46610.24721370.247212079X-RAY DIFFRACTION95
2.4661-2.65630.2651470.253712186X-RAY DIFFRACTION96
2.6563-2.92330.26441450.253612445X-RAY DIFFRACTION98
2.9233-3.34550.23651510.225312607X-RAY DIFFRACTION99
3.3455-4.21190.23641510.198712801X-RAY DIFFRACTION99

+
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