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- PDB-7o4u: Structure of the alpha subunit of Mycobacterium tuberculosis beta... -

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Basic information

Entry
Database: PDB / ID: 7o4u
TitleStructure of the alpha subunit of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with oxidized nicotinamide adenine dinucleotide
Components3-hydroxyacyl-CoA dehydrogenase
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 / fatty acid beta-oxidation / NAD+ binding / 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 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / diffrn_source / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation_author.name ..._citation.journal_volume / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _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 ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,3384
Polymers156,0122
Non-polymers1,3272
Water25214
1
A: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6692
Polymers78,0061
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6692
Polymers78,0061
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.812, 86.913, 88.957
Angle α, β, γ (deg.)88.021, 89.915, 75.192
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase /


Mass: 78005.805 Da / Num. of mol.: 2
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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.3 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 22% PEG 4000, 0.1 M TEA pH 7.5, 20% IPA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→88.9 Å / Num. obs: 38685 / % possible obs: 97.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 59.37 Å2 / CC1/2: 0.988 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.82 Å / Num. unique obs: 4735 / CC1/2: 0.867

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B3H

4b3h


Resolution: 2.7→88.9 Å / SU ML: 0.4947 / Cross valid method: FREE R-VALUE / σ(F): 0.72 / Phase error: 30.8834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2699 1982 5.13 %
Rwork0.2128 36669 -
obs0.2157 38651 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→88.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10515 0 88 14 10617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210816
X-RAY DIFFRACTIONf_angle_d0.463614667
X-RAY DIFFRACTIONf_chiral_restr0.03961669
X-RAY DIFFRACTIONf_plane_restr0.00411923
X-RAY DIFFRACTIONf_dihedral_angle_d14.86193998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.37831530.32512673X-RAY DIFFRACTION98.02
2.77-2.840.38111390.29492569X-RAY DIFFRACTION97.38
2.84-2.930.35711530.28332644X-RAY DIFFRACTION97.56
2.93-3.020.34871620.26672544X-RAY DIFFRACTION97.37
3.02-3.130.39241260.27442652X-RAY DIFFRACTION97.27
3.13-3.250.31451350.27682597X-RAY DIFFRACTION97.05
3.25-3.40.33951490.25072577X-RAY DIFFRACTION96.19
3.4-3.580.31561530.24182599X-RAY DIFFRACTION97
3.58-3.810.3231420.21852631X-RAY DIFFRACTION97.43
3.81-4.10.21161300.20062643X-RAY DIFFRACTION98.82
4.1-4.510.24211440.17962643X-RAY DIFFRACTION98.48
4.51-5.160.23521350.18422636X-RAY DIFFRACTION98.44
5.16-6.510.21891240.20022646X-RAY DIFFRACTION97.98
6.51-88.90.18531370.15722615X-RAY DIFFRACTION96.94
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)
13.27877621535-0.1063819344090.8818233456923.59908046231-0.2973159082962.941015701380.218797516655-0.642727392497-0.3401762627250.355346041017-0.176856160531-0.008411175702390.0543453632350.0976290133952-0.02443818050270.343167794848-0.0198337333558-0.01554881795870.4719657356110.06469085141090.31844999925211.8516014315-4.48464931747-34.4117940023
22.639727077890.552893174041-0.8951828964492.655824413020.4766182369382.211087876080.286509145016-0.8127045086680.3721201323161.24236319252-0.3107534243510.650949338990.464758255521-0.343365016956-0.02882060388220.943824640743-0.1483625120080.1939984532760.719682486481-0.1327523279780.561836324036-5.0386867080530.61753938-18.7332397665
33.40840589139-0.54716836418-0.250367814972.37586144740.5542881433383.083884535120.0611352710972-0.07312119644440.3801866476330.102698048561-0.08261331552740.446151729266-0.298485009555-0.5483212989560.02713326769330.4235706724680.08850794240660.07699669472650.390847547109-0.005902242795820.512180659384-10.802877451931.9612293943-46.1642688286
42.680725299530.0598857845819-0.5458688393822.915453688430.05816041278762.005758461910.2027236777430.5493645319730.0988521960381-0.7088781561-0.212357192186-0.179119531042-0.2243081135530.0230335113243-0.008751471286430.4983747072710.08564312589630.02465188287910.5003667088310.01250900580690.3352078660313.05350298918.8991262964-76.9174935317
51.475049444070.8073646837031.391217210973.941952842241.774570765272.38512895058-0.01421146144010.433888999402-0.310464171778-0.8882076865710.3517585839510.1553454125540.04733505387090.245299177574-0.3014256167340.640573089831-0.0477345773877-0.08966305855110.621468372746-0.01511986223250.434990521861-2.22169672797-21.9895387252-88.1098628909
63.178119383990.446002349090.5661310849252.383982100460.5011946417982.503841230690.0818934770705-0.281329084493-0.274721885995-0.00385579162844-0.04541529703590.1266292344220.175543407449-0.225014389632-0.03661719364240.36165797550.0133238872748-0.08335451310270.3053820352240.01648415974530.376762479041-10.3489660442-27.992710845-64.3991406153
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 291 )AA3 - 2911 - 284
22chain 'A' and (resid 292 through 510 )AA292 - 510285 - 503
33chain 'A' and (resid 511 through 720 )AA511 - 720504 - 713
44chain 'B' and (resid 3 through 259 )BC3 - 2591 - 250
55chain 'B' and (resid 260 through 510 )BC260 - 510251 - 501
66chain 'B' and (resid 511 through 720 )BC511 - 720502 - 713

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