[English] 日本語
Yorodumi
- PDB-7f74: Rv3094c in complex with FMN. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f74
TitleRv3094c in complex with FMN.
ComponentsRv3094c
KeywordsOXIDOREDUCTASE / sulfoxidation / ethionamide / Mycobacterium tuberculosis
Function / homology
Function and homology information


fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Hydroxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Z.X. / Ouyang, S.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2018ZX10101004 China
National Natural Science Foundation of China (NSFC)31570875
CitationJournal: Commun Biol / Year: 2023
Title: Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene.
Authors: Wan, L. / Hu, P. / Zhang, L. / Wang, Z.X. / Fleming, J. / Ni, B. / Luo, J. / Guan, C.X. / Bai, L. / Tan, Y. / Liu, H. / Li, N. / Xiao, T. / Bai, H. / Zhang, Y.A. / Zhang, X.E. / Wan, K. / ...Authors: Wan, L. / Hu, P. / Zhang, L. / Wang, Z.X. / Fleming, J. / Ni, B. / Luo, J. / Guan, C.X. / Bai, L. / Tan, Y. / Liu, H. / Li, N. / Xiao, T. / Bai, H. / Zhang, Y.A. / Zhang, X.E. / Wan, K. / Bi, L. / Ouyang, S. / Zhang, H.
History
DepositionJun 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Rv3094c
B: Rv3094c
C: Rv3094c
D: Rv3094c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2048
Polymers161,3794
Non-polymers1,8254
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-99 kcal/mol
Surface area51170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.058, 134.223, 109.411
Angle α, β, γ (deg.)90.000, 128.930, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Rv3094c


Mass: 40344.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv3094c / Production host: Escherichia coli (E. coli) / References: UniProt: O05773
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 289.15 K / Method: liquid diffusion
Details: 0.2M sodium nitrate, 0.1M Bis Tris propane pH=8.5, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 289.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→42.55 Å / Num. obs: 123413 / % possible obs: 94.55 % / Redundancy: 1.9 % / CC1/2: 0.995 / Net I/σ(I): 9.19
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 12343 / CC1/2: 0.929

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCF

4kcf


Resolution: 2→42.55 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 6117 4.96 %
Rwork0.1899 117296 -
obs0.192 123413 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.18 Å2 / Biso mean: 41.3775 Å2 / Biso min: 16.17 Å2
Refinement stepCycle: final / Resolution: 2→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11176 0 148 676 12000
Biso mean--71.04 37.21 -
Num. residues----1485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.32612180.279241054323100
2.02-2.040.33642030.285141004303100
2.04-2.070.46832010.37973612381387
2.07-2.10.45271730.33883704387790
2.1-2.120.32342430.25124029427299
2.12-2.150.32632120.23864130434299
2.15-2.180.29152220.23534077429999
2.18-2.220.29582130.23724036424999
2.22-2.230.306980.2451930202891
2.27-2.290.29681240.23692247237194
2.29-2.330.27092400.22154024426499
2.33-2.370.25162230.2134099432299
2.37-2.410.26562170.193840764293100
2.41-2.460.24942030.186741394342100
2.46-2.520.25691870.19474103429099
2.52-2.580.23392410.18694070431199
2.58-2.640.28312210.17941124333100
2.64-2.710.23411890.20073847403693
2.71-2.790.24162170.18534097431499
2.79-2.880.26162300.18864050428098
2.88-2.980.23941590.19314146430599
2.98-3.10.23632150.18694107432299
3.1-3.240.23041910.18634097428899
3.24-3.420.21082240.18554132435699
3.42-3.630.20162370.18343918415595
3.63-3.910.18961660.17813872403892
3.91-4.30.211900.15384103429399
4.3-4.920.17462520.14744108436099
4.93-6.20.1982110.16744123433499
6.2-42.550.19211970.17754103430096

+
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