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- PDB-8pwz: Crystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadBD from ... -

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Basic information

Entry
Database: PDB / ID: 8pwz
TitleCrystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadBD from Mycobacterium tuberculosis
Components
  • (3R)-hydroxyacyl-ACP dehydratase subunit HadB
  • UPF0336 protein Rv0504c
KeywordsLYASE / (3R)-hydroxyacyl-ACP dehydratase / FAS-II system / Mycolic acid synthesis
Function / homology
Function and homology information


(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / plasma membrane
Similarity search - Function
Dehydratase subunit HadA-like / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily
Similarity search - Domain/homology
(3R)-hydroxyacyl-ACP dehydratase subunit HadB / UPF0336 protein Rv0504c
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00196723217 Å
AuthorsRima, J. / Grimoire, Y. / Bories, P. / Bardou, F. / Quemard, A. / Bon, C. / Mourey, L. / Tranier, S.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Protein Sci. / Year: 2024
Title: HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function.
Authors: Bories, P. / Rima, J. / Tranier, S. / Marcoux, J. / Grimoire, Y. / Tomaszczyk, M. / Launay, A. / Fata, K. / Marrakchi, H. / Burlet-Schiltz, O. / Mourey, L. / Ducoux-Petit, M. / Bardou, F. / Bon, C. / Quemard, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0336 protein Rv0504c
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB


Theoretical massNumber of molelcules
Total (without water)35,5072
Polymers35,5072
Non-polymers00
Water34219
1
A: UPF0336 protein Rv0504c
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB

A: UPF0336 protein Rv0504c
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB


Theoretical massNumber of molelcules
Total (without water)71,0144
Polymers71,0144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area7480 Å2
ΔGint-32 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.646, 96.646, 143.921
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein UPF0336 protein Rv0504c


Mass: 20557.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv0504c, MTCY20G9.31c / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFK3
#2: Protein (3R)-hydroxyacyl-ACP dehydratase subunit HadB


Mass: 14949.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: hadB, Rv0636 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6WYY7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.84 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0,1 M NaCacodylate pH 6,5, 40% MPD and 5% PEG 8k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.892→83.698 Å / Num. obs: 14207 / % possible obs: 94.7 % / Redundancy: 18.6 % / Biso Wilson estimate: 43.4800802836 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.014 / Rrim(I) all: 0.057 / Net I/σ(I): 27.3
Reflection shellResolution: 1.892→2.216 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.247 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 711 / CC1/2: 0.942 / Rpim(I) all: 0.287 / Rrim(I) all: 1.112 / % possible all: 75.6

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Processing

Software
NameVersionClassification
MxCuBE1.9_1692+SVNdata collection
PHENIX1.9_1692+SVNrefinement
autoPROCdata processing
STARANISO2.3.24data scaling
Coot0.9.8.7model building
XDSdata reduction
XDSdata scaling
PHASERversion 2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.00196723217→54.5657301655 Å / SU ML: 0.256068176251 / Cross valid method: FREE R-VALUE / σ(F): 1.36415165716 / Phase error: 40.5265965416
RfactorNum. reflection% reflection
Rfree0.290455304595 1415 10.0056569085 %
Rwork0.246052592853 12727 -
obs0.250484525568 14142 51.5303891561 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.9591451609 Å2
Refinement stepCycle: LAST / Resolution: 2.00196723217→54.5657301655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 0 19 2166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003649141356362196
X-RAY DIFFRACTIONf_angle_d0.7620808240452985
X-RAY DIFFRACTIONf_chiral_restr0.0300435654885341
X-RAY DIFFRACTIONf_plane_restr0.00361342669357386
X-RAY DIFFRACTIONf_dihedral_angle_d13.1916183076790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.07350.375710817763130.391992127802117X-RAY DIFFRACTION4.88721804511
2.0735-2.15650.437231579345280.392470480148245X-RAY DIFFRACTION10.182767624
2.1565-2.25470.435848212516400.389983071532374X-RAY DIFFRACTION15.3903345725
2.2547-2.37360.373546911733580.359818992033520X-RAY DIFFRACTION21.47102526
2.3736-2.52230.382101122822860.362583448042764X-RAY DIFFRACTION31.6220238095
2.5223-2.7170.4227707451221260.3348106640691131X-RAY DIFFRACTION46.07771261
2.717-2.99040.3514985220422110.3102025270421903X-RAY DIFFRACTION77.4642726273
2.9904-3.42310.3319329116562740.2815499762172466X-RAY DIFFRACTION99.8178506375
3.4231-4.31250.2819424585772800.2277662142372524X-RAY DIFFRACTION99.9287241625
4.3125-54.5650.2420396455372990.2061790102142683X-RAY DIFFRACTION99.9329758713
Refinement TLS params.Method: refined / Origin x: -22.7855928553 Å / Origin y: -29.578603308 Å / Origin z: -0.0178486222433 Å
111213212223313233
T0.785776184368 Å20.0457011959001 Å20.167324679815 Å2-0.00984809727043 Å2-0.00803037259527 Å2--0.236170173003 Å2
L2.66645610299 °20.702353771311 °2-0.17542642647 °2-2.75708225044 °2-1.93253722589 °2--4.59920182567 °2
S0.243422948439 Å °0.0520188202958 Å °-0.0433880225489 Å °-0.286701677716 Å °-0.0707924584903 Å °-0.243665352729 Å °-1.42250754602 Å °-0.26144632568 Å °-0.118541899999 Å °
Refinement TLS groupSelection details: all

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