[English] 日本語
Yorodumi
- PDB-8x74: Crystal structure of ZmHSL1A complexed with mesotrione -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x74
TitleCrystal structure of ZmHSL1A complexed with mesotrione
Components2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
KeywordsOXIDOREDUCTASE / Complex / Enzyme
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
Chem-92L / 2-OXOGLUTARIC ACID / : / 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.791 Å
AuthorsLin, H.-Y. / Dong, J. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: An artificially evolved gene for herbicide-resistant rice breeding.
Authors: Dong, J. / Yu, X.H. / Dong, J. / Wang, G.H. / Wang, X.L. / Wang, D.W. / Yan, Y.C. / Xiao, H. / Ye, B.Q. / Lin, H.Y. / Yang, G.F.
History
DepositionNov 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2934
Polymers39,7481
Non-polymers5443
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.866, 53.452, 75.571
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein / HPPD Inhibitor Sensitive 1-like 1 protein


Mass: 39748.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100285776
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B6U9L0
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-92L / 2-[(4-methylsulfonyl-2-nitro-phenyl)-oxidanyl-methylidene]cyclohexane-1,3-dione / Mesotrione


Mass: 339.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13NO7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.06 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.79→40 Å / Num. obs: 33389 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 19.48
Reflection shellResolution: 1.79→1.84 Å / Rmerge(I) obs: 0.415 / Num. unique obs: 2508 / CC1/2: 0.859

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.791→34.23 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1670 5 %
Rwork0.1803 --
obs0.1821 33389 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.791→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 34 268 3009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072804
X-RAY DIFFRACTIONf_angle_d0.9923804
X-RAY DIFFRACTIONf_dihedral_angle_d18.2371698
X-RAY DIFFRACTIONf_chiral_restr0.096416
X-RAY DIFFRACTIONf_plane_restr0.006497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.791-1.84320.30091360.25882580X-RAY DIFFRACTION97
1.8432-1.90270.31911390.22242630X-RAY DIFFRACTION100
1.9027-1.97070.24691380.20982621X-RAY DIFFRACTION100
1.9707-2.04960.23541380.20892633X-RAY DIFFRACTION100
2.0496-2.14290.22811390.22641X-RAY DIFFRACTION100
2.1429-2.25580.24881390.19042631X-RAY DIFFRACTION100
2.2558-2.39710.22681390.18892634X-RAY DIFFRACTION100
2.3971-2.58220.24161400.20122663X-RAY DIFFRACTION100
2.5822-2.84190.23481390.1842644X-RAY DIFFRACTION100
2.8419-3.25290.19661390.18362648X-RAY DIFFRACTION100
3.2529-4.09720.19781420.15962688X-RAY DIFFRACTION100
4.0972-34.230.18941420.15512706X-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