[English] 日本語
Yorodumi
- PDB-6wta: Structure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wta
TitleStructure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027 in complex with F420
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / F420 / Complex / Cofactor
Function / homologyF420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / coenzyme F420 binding / FMN-binding split barrel / oxidoreductase activity / plasma membrane / COENZYME F420-4 / Nitroreductase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsJackson, C.J. / Antoney, J.P.
Citation
Journal: J.Mol.Biol. / Year: 2025
Title: A F 420 -dependent single domain chemogenetic tool for protein de-dimerization.
Authors: Antoney, J. / Kainrath, S. / Dubowsky, J.G. / Ahmed, F.H. / Kang, S.W. / Mackie, E.R.R. / Granado, G.B. / Soares da Costa, T.P. / Jackson, C.J. / Janovjak, H.
#1: Journal: Biorxiv / Year: 2022
Title: A F420-dependent single domain chemogenetic tool for protein de-dimerization
Authors: Antoney, J. / Kainrath, S. / Ahmed, F.H. / Kang, S.W. / Mackie, E.R. / Soares da Costa, T.P. / Jackson, C.J. / Janovjak, H.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3May 14, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
Z: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0883
Polymers32,0562
Non-polymers1,0321
Water1,56787
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0602
Polymers16,0281
Non-polymers1,0321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
Z: Uncharacterized protein


  • defined by author&software
  • 16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)16,0281
Polymers16,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.364, 63.022, 65.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Uncharacterized protein


Mass: 16028.034 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2027 / Plasmid: pETMCSIII / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QU01
#2: Chemical ChemComp-UBM / COENZYME F420-4 / (2~{S})-2-[[(4~{S})-5-oxidanyl-5-oxidanylidene-4-[[(4~{S})-5-oxidanyl-5-oxidanylidene-4-[[(4~{S})-5-oxidanyl-5-oxidanyl idene-4-[[(2~{S})-2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[8-oxidanyl-2,4-bis(oxidanylidene)-1~{H}-pyrim ido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxypropanoyl]amino]pentanoyl]amino]pentanoyl]amino]pentanoyl]amino]pentanedi oic acid


Mass: 1031.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C39H50N7O24P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 0.07 M citrate, 0.03 M bis-tris propane, 16% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953729987144 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953729987144 Å / Relative weight: 1
ReflectionResolution: 1.67→32.68 Å / Num. obs: 17596 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 19.79 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.078 / Rrim(I) all: 0.183 / Χ2: 0.93 / Net I/σ(I): 11.8
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.556 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 886 / CC1/2: 0.91 / Rpim(I) all: 0.511 / Χ2: 1.02 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
XDS20200131data reduction
Aimless1.11.21data scaling
PHASER2.8.3phasing
Coot0.8.6.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y9I

4y9i


Resolution: 1.67→32.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 907 5.2 %
Rwork0.2002 --
obs0.2022 17438 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 71 87 1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041283
X-RAY DIFFRACTIONf_angle_d0.6831751
X-RAY DIFFRACTIONf_dihedral_angle_d20.681470
X-RAY DIFFRACTIONf_chiral_restr0.046186
X-RAY DIFFRACTIONf_plane_restr0.004225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.770.40851490.37852722X-RAY DIFFRACTION100
1.77-1.910.30541560.27362686X-RAY DIFFRACTION99
1.91-2.10.28561520.2332670X-RAY DIFFRACTION98
2.1-2.410.23741570.2042738X-RAY DIFFRACTION99
2.41-3.030.26311380.18692791X-RAY DIFFRACTION100
3.03-32.680.18191550.16572924X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16270.35660.1240.7830.24180.9944-0.0748-0.07830.1012-0.14460.2369-0.22160.38740.3042-0.00080.62440.07140.07510.3121-0.19840.8615-24.0656111.402666.7058
25.5780.2773-0.83423.6018-2.07052.16050.03970.2726-0.33820.0422-0.0102-0.12520.11010.4939-0.10820.26620.01180.0030.359-0.04510.2507-21.4152118.668769.8868
35.1969-0.1391.32072.5693-0.73887.66990.0815-0.10360.0060.10230.12020.0575-0.06-0.1178-0.19210.17820.02080.00780.1810.02480.1875-29.8737124.4677.3376
45.00421.22330.02442.03660.56243.4080.09090.11180.16320.09250.01340.3099-0.2438-0.5766-0.05640.23560.07880.03190.40050.04240.2399-36.6807126.755276.0896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Z' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 140 )

+
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