[English] 日本語
Yorodumi
- PDB-6zyk: Non-heme monooxygenase, ThoJ-Ni complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zyk
TitleNon-heme monooxygenase, ThoJ-Ni complex
ComponentsMonooxygenase
KeywordsMETAL BINDING PROTEIN / non-heme monooxygenase
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / NICKEL (II) ION / L(+)-TARTARIC ACID / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesStreptomyces malaysiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO4116_3_1 Germany
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Non-Heme Monooxygenase ThoJ Catalyzes Thioholgamide beta-Hydroxylation.
Authors: Sikandar, A. / Lopatniuk, M. / Luzhetskyy, A. / Koehnke, J.
History
DepositionAug 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7873
Polymers33,5781
Non-polymers2092
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-11 kcal/mol
Surface area10550 Å2
Unit cell
Length a, b, c (Å)80.753, 80.753, 129.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Monooxygenase


Mass: 33578.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces malaysiense (bacteria) / Gene: VT52_024865
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1J4PXK4
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 150 mM Sodium tartrate, 28% (w/v) PEG 3350, 10% (v/v) 2.0 M NDSB-221

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→68.56 Å / Num. obs: 14610 / % possible obs: 99.94 % / Redundancy: 2 % / Rrim(I) all: 0.1201 / Net I/σ(I): 9.4
Reflection shellResolution: 2.55→2.64 Å / Num. unique obs: 1414 / Rrim(I) all: 0.9535

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
xia2data reduction
Aimlessdata scaling
Phaser-MRphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NCJ

5ncj


Resolution: 2.55→42.86 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 702 4.81 %
Rwork0.2271 --
obs0.2277 14600 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 11 56 1939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041933
X-RAY DIFFRACTIONf_angle_d0.7562638
X-RAY DIFFRACTIONf_dihedral_angle_d16.452268
X-RAY DIFFRACTIONf_chiral_restr0.052297
X-RAY DIFFRACTIONf_plane_restr0.006348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.750.32611170.31282726X-RAY DIFFRACTION100
2.75-3.020.32071380.27232719X-RAY DIFFRACTION100
3.02-3.460.28261400.24972748X-RAY DIFFRACTION100
3.46-4.360.20891390.19962785X-RAY DIFFRACTION100
4.36-42.860.20241680.20272920X-RAY DIFFRACTION100

+
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