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- PDB-7f74: Rv3094c in complex with FMN. -

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Basic information

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


3-methylbutanoyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / L-leucine catabolic process / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 3.07 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

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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: 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

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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

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