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- PDB-7f70: Crystal structure of Rv3094c -

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Basic information

Entry
Database: PDB / ID: 7f70
TitleCrystal structure of Rv3094c
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
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsWang, Z.X. / Ouyang, S.Y. / Zhang, H.T.
Funding support China, 6items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29020000 China
National Science Foundation (NSF, China)2018ZX10101004 China
National Natural Science Foundation of China (NSFC)31770148 China
National Natural Science Foundation of China (NSFC)31770150 China
National Natural Science Foundation of China (NSFC)31770948 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 26, 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

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Assembly

Deposited unit
A: Rv3094c


Theoretical massNumber of molelcules
Total (without water)40,3451
Polymers40,3451
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15580 Å2
Unit cell
Length a, b, c (Å)134.322, 134.322, 110.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Rv3094c


Mass: 40344.691 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.43 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_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: 2.14→85.16 Å / Num. obs: 49234 / % possible obs: 93.05 % / Redundancy: 2 % / Biso Wilson estimate: 37.75 Å2 / CC1/2: 0.708 / Net I/σ(I): 7.53
Reflection shellResolution: 2.14→2.217 Å / Num. unique obs: 2750 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.15.2_3472phasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCF

4kcf


Resolution: 2.14→85.16 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3785 7.69 %RANDOM
Rwork0.194 45449 --
obs0.1963 49234 92.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.99 Å2 / Biso mean: 41.7886 Å2 / Biso min: 18.83 Å2
Refinement stepCycle: final / Resolution: 2.14→85.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 0 166 2923
Biso mean---45.59 -
Num. residues----365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.170.24051480.23331814196299
2.17-2.20.30891480.23051833198199
2.2-2.230.29081480.24681757190599
2.23-2.230.2828410.240150554693
2.27-2.290.3331990.34081133123289
2.29-2.330.38841460.28771762190897
2.33-2.360.27091480.238117951943100
2.36-2.410.25551500.23031825197599
2.41-2.450.24761510.228417891940100
2.45-2.50.2811530.222318441997100
2.5-2.550.27051430.23271738188196
2.55-2.60.23891490.19761803195299
2.6-2.650.22611250.20451489161498
2.7-2.730.3298630.265179385690
2.73-2.80.20231570.18941824198199
2.8-2.890.22241550.19641796195199
2.89-2.980.21951490.205617971946100
2.98-3.090.21361490.194918151964100
3.09-3.210.21491560.196418141970100
3.21-3.360.21871490.19821798194799
3.36-3.530.25191480.211118351983100
3.53-3.750.21811490.188717811930100
3.75-4.040.20471490.17618542003100
4.04-4.450.22481520.153218031955100
4.45-5.090.14991520.163218161968100
5.1-6.420.21771530.17818211974100
6.42-85.160.18551550.158918151970100

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