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- PDB-7f72: Rv3094c in complex with FAD and ETH. -

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Basic information

Entry
Database: PDB / ID: 7f72
TitleRv3094c in complex with FAD and ETH.
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
2-ethylpyridine-4-carboximidothioic acid / FLAVIN MONONUCLEOTIDE / Hydroxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 China
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 1.0Jul 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rv3094c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9813
Polymers40,3591
Non-polymers6232
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.100, 134.100, 109.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-640-

HOH

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Components

#1: Protein Rv3094c


Mass: 40358.715 Da / Num. of mol.: 1 / Mutation: S252T
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-1JA / 2-ethylpyridine-4-carboximidothioic acid


Mass: 166.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.7 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
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.

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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: 1.64→27.38 Å / Num. obs: 60945 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 25.8
Reflection shellResolution: 1.64→1.699 Å / Num. unique obs: 6039 / CC1/2: 0.852

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCF

4kcf


Resolution: 1.64→27.379 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 2959 4.86 %
Rwork0.1853 57984 -
obs0.1865 60943 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.68 Å2 / Biso mean: 43.9045 Å2 / Biso min: 21.51 Å2
Refinement stepCycle: final / Resolution: 1.64→27.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 73 140 2998
Biso mean--58.52 39.25 -
Num. residues----370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.670.28181490.237927352884100
1.67-1.70.25491460.227627152861100
1.7-1.730.2361390.230127192858100
1.73-1.760.24841390.207427292868100
1.76-1.80.24151510.207327472898100
1.8-1.830.23681250.205527172842100
1.83-1.880.25921340.207227302864100
1.88-1.920.30941530.261327462899100
1.92-1.980.24271130.224827532866100
1.98-2.030.22121390.19827362875100
2.03-2.10.21400.203227562896100
2.1-2.180.21071380.189327172855100
2.18-2.260.23031250.201427762901100
2.26-2.360.24931240.186727832907100
2.37-2.490.22581300.180827862916100
2.49-2.650.2361540.182227302884100
2.65-2.850.21211440.188727772921100
2.85-3.140.20941540.189127842938100
3.14-3.590.21731610.188627842945100
3.59-4.520.17651690.155228042973100
4.52-27.380.18681320.18142960309299

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