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- PDB-7o4q: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 7o4q
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in space group C2221 (unliganded)
Components
  • 3-hydroxyacyl-CoA dehydrogenase
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / trifunctional enzyme / fatty acid beta oxidation / mycobacterium tuberculosis
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid beta-oxidation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
: / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site ...: / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDalwani, S. / Wierenga, R.K. / Venkatesan, R.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland293369 Finland
Academy of Finland289024 Finland
Academy of Finland319194 Finland
Citation
Journal: J.Struct.Biol. / Year: 2021
Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.
Authors: Dalwani, S. / Lampela, O. / Leprovost, P. / Schmitz, W. / Juffer, A.H. / Wierenga, R.K. / Venkatesan, R.
#1: Journal: ACS Chem Biol / Year: 2013
Title: Structure of Mycobacterial Beta-Oxidation Trifunctional Enzyme Reveals its Altered Assembly and Putative Substrate Channeling Pathway
Authors: Venkatesan, R. / Wierenga, R.K.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation_author.name / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Jan 31, 2024Group: 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
B: 3-hydroxyacyl-CoA dehydrogenase
C: Putative acyltransferase Rv0859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,03629
Polymers120,4662
Non-polymers2,57027
Water6,179343
1
B: 3-hydroxyacyl-CoA dehydrogenase
C: Putative acyltransferase Rv0859
hetero molecules

B: 3-hydroxyacyl-CoA dehydrogenase
C: Putative acyltransferase Rv0859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,07258
Polymers240,9324
Non-polymers5,14054
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Unit cell
Length a, b, c (Å)104.087, 204.685, 132.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase


Mass: 78005.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadB, Rv0860 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53872, 3-hydroxyacyl-CoA dehydrogenase
#2: Protein Putative acyltransferase Rv0859


Mass: 42460.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fadA, Rv0859 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.9 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5 / Details: 2M (NH4)2SO4, 100mM MOPS pH 6.5, 10% Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→48.45 Å / Num. obs: 160514 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.22 Å / Num. unique obs: 4363 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B3H

4b3h


Resolution: 2.1→48.45 Å / SU ML: 0.218 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 2093 1.3 %
Rwork0.1949 158368 -
obs0.1953 160461 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8350 0 141 343 8834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228669
X-RAY DIFFRACTIONf_angle_d0.490811753
X-RAY DIFFRACTIONf_chiral_restr0.04121324
X-RAY DIFFRACTIONf_plane_restr0.00361529
X-RAY DIFFRACTIONf_dihedral_angle_d14.0343166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.32761360.286710182X-RAY DIFFRACTION95.76
2.14-2.20.23741410.251610580X-RAY DIFFRACTION99.95
2.2-2.260.47641390.370810580X-RAY DIFFRACTION99.64
2.26-2.320.27361370.291410506X-RAY DIFFRACTION99.33
2.32-2.40.23441390.227210579X-RAY DIFFRACTION100
2.4-2.480.24431380.22110617X-RAY DIFFRACTION99.94
2.48-2.580.24141420.219710586X-RAY DIFFRACTION99.93
2.58-2.70.25151400.215810609X-RAY DIFFRACTION99.99
2.7-2.840.27361410.21910579X-RAY DIFFRACTION99.98
2.84-3.020.25031370.223710635X-RAY DIFFRACTION100
3.02-3.250.21441410.216910592X-RAY DIFFRACTION99.94
3.25-3.580.22271390.185610611X-RAY DIFFRACTION99.85
3.58-4.10.19361390.155710555X-RAY DIFFRACTION99.86
4.1-5.160.16051420.135710582X-RAY DIFFRACTION99.88
5.17-48.450.17231420.158210575X-RAY DIFFRACTION99.73
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)
14.64089679678-3.04184175059-1.136826302498.741385380571.498078224766.643844702170.114461543980.1176760864280.3978069173240.097407821432-0.1603105404440.14062202791-0.856881893947-0.1058905658230.001765652882740.35651727656-0.07853189158890.05708759083890.2924563876030.05342458161350.231724553009157.61577632432.1516003114107.607024525
21.398803739920.147188410347-0.9276712200640.777675020238-0.1295652350142.338819114980.0169167183766-0.193929595101-0.01800895112350.028819555483-0.0598323187603-0.162652013472-0.2179708515120.4575343782970.0440061567710.259826834607-0.0784783270942-0.02622070041190.2984655455650.008784875603460.253872653555153.51054725924.8262153385124.452342874
30.3187297268160.2413313776540.642395716630.8654205287870.8997661087741.39718061637-0.2001388869320.04085255385850.103557489843-0.399100819540.0846694762534-0.099337825473-0.5915711583150.1009383067360.09056773311160.47216705802-0.0680971889353-0.003977824983820.2997319943040.0148080362260.298030934916147.44753188544.5211175832129.961823102
44.41281514694-1.375369589320.5819618931872.214831084590.01086279185652.48604903759-0.127745656357-0.1052821468550.290662450678-0.1421231733660.0423695653139-0.0834234463438-0.3610965943580.03902059879770.06851347061060.311521262379-0.0592694826635-0.04735097322960.220105511237-0.01587427104430.30042890009158.87816622755.5322445234152.973838599
51.513695410560.358044613809-0.05151444722740.9762610461710.2137737744220.747428523067-0.0829548241691-0.009872680698950.152737533984-0.123481804294-0.02724697690880.0977620156089-0.0749988659928-0.1065623416590.1136502808420.433088662880.0457754099984-0.09518977292130.263681451259-0.03405216239220.30224608862132.72695519350.4323955505148.001691691
64.96707593349-1.493445061131.407457111532.91138493423-0.7049107104433.34104160305-0.1002146561350.1269733785670.1084497884490.03431870787670.107795001345-0.01646385768590.00426835113998-0.0623554876208-0.001598328857720.213797154333-0.01550983519630.05310567455180.1400680434190.005337772098010.116807360494119.907236899-10.0707035208147.589061262
72.35650424642-0.3834848697730.3385435852192.01753840767-0.5339996521742.93894064519-0.0486995893142-0.0340678832912-0.125354728245-0.05698334637460.07538780288760.1363599513380.295181491907-0.187690479534-0.02867539031950.257079878663-0.004526746211790.02627919082670.2294922168470.01548214002750.189846613358117.833464073-9.22278754424137.382795449
87.532738627692.07046322509-6.112305605320.577582246655-1.686487821654.95188414212-0.1207158162020.3029979011620.1593931491480.1306032566370.191061145668-0.1057184520730.0950208794188-0.315590854209-0.02338722779120.4119519527880.007139860525530.01492760017650.1814452808280.008793831810750.291918850434127.84997951817.9666190575146.752011438
90.995988226865-0.306789374886-0.02585602010353.549868179770.2657308880941.66013245964-0.137214547455-0.206638328651-0.0245432143710.5738947067020.09898329331960.211735449267-0.0320646542434-0.1373131162570.05325650162420.3244736765170.04478494584060.02748472653590.3006759579480.04727090673610.173488036699121.88774633-8.26915528837159.999345098
104.215587667183.524653369235.269406775294.226101117125.496007215197.88820398966-0.00039323532235-0.2712945231080.1427785962961.08529432909-0.04088930375-0.381574695090.0885750663156-0.03871511341930.1344116277420.4150465797550.0815527507508-0.02626688526450.3436620275820.01687727762270.313013160012130.8268363310.0422491028354164.096146682
110.2711981980550.36571243075-0.4385354369184.39642441943-3.674059075833.29517655201-0.0275868946876-0.0599813119360.08475490738630.369557908805-0.0365179017537-0.428545450791-0.3685713141520.1973791064390.06957807007430.365183781228-0.0228035383917-0.03368883358610.280571137041-0.03138019426060.285148758538130.18044808518.2371961151153.195650975
121.516293878930.1288006604430.04116945640531.799186176070.09532804564182.23836582909-0.0452585367212-0.03467863140920.07571146897960.2087459485140.1345058959030.272148571366-0.116624226651-0.308881987356-0.08454151482150.2944391285470.04144367437390.06738522511070.3375532698230.04242037462930.263729174152109.9210227921.94311064657151.084225175
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid -13 through 47 )BA-13 - 471 - 53
22chain 'B' and (resid 48 through 275 )BA48 - 27554 - 283
33chain 'B' and (resid 276 through 334 )BA276 - 334284 - 345
44chain 'B' and (resid 335 through 471 )BA335 - 471346 - 484
55chain 'B' and (resid 472 through 720 )BA472 - 720485 - 737
66chain 'C' and (resid 2 through 27 )CD2 - 271 - 26
77chain 'C' and (resid 28 through 132 )CD28 - 13227 - 132
88chain 'C' and (resid 133 through 163 )CD133 - 163133 - 163
99chain 'C' and (resid 164 through 203 )CD164 - 203164 - 205
1010chain 'C' and (resid 204 through 226 )CD204 - 226206 - 228
1111chain 'C' and (resid 227 through 261 )CD227 - 261229 - 263
1212chain 'C' and (resid 262 through 403 )CD262 - 403264 - 407

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