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- PDB-8y21: Crystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB heter... -

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Basic information

Entry
Database: PDB / ID: 8y21
TitleCrystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium tuberculosis complexed with substrate Palmitoyl-CoA
Components((3R)-hydroxyacyl-ACP dehydratase subunit ...) x 2
KeywordsLYASE / fatty acid synthesis
Function / homology
Function and homology information


(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acid biosynthetic process / plasma membrane
Similarity search - Function
: / Dehydratase subunit HadA-like / : / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily
Similarity search - Domain/homology
COENZYME A / DI(HYDROXYETHYL)ETHER / PALMITIC ACID / (3R)-hydroxyacyl-ACP dehydratase subunit HadB / UPF0336 protein Rv0635
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.691 Å
AuthorsGanguly, S.S. / Singh, B.K. / Saha, R. / De, S. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR40990/MED/29/1540/2020 India
CitationJournal: To Be Published
Title: Crystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium tuberculosis complexed with substrate Palmitoyl-CoA
Authors: Ganguly, S.S. / Singh, B.K. / Saha, R. / De, S. / Das, A.K.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: (3R)-hydroxyacyl-ACP dehydratase subunit HadA
D: (3R)-hydroxyacyl-ACP dehydratase subunit HadA
E: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
F: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,36412
Polymers66,5534
Non-polymers1,8118
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.169, 78.303, 109.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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(3R)-hydroxyacyl-ACP dehydratase subunit ... , 2 types, 4 molecules CDEF

#1: Protein (3R)-hydroxyacyl-ACP dehydratase subunit HadA


Mass: 18326.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv0635 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFK1
#2: Protein (3R)-hydroxyacyl-ACP dehydratase subunit HadB


Mass: 14949.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv0636 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: I6WYY7

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Non-polymers , 4 types, 198 molecules

#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 43.77 % / Description: Long rod shaped crystal
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 200 mM Ammonium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.69→36.85 Å / Num. obs: 65768 / % possible obs: 91.45 % / Redundancy: 2 % / Biso Wilson estimate: 16.45 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.01715 / Rpim(I) all: 0.01715 / Rrim(I) all: 0.02425 / Net I/σ(I): 24.48
Reflection shellResolution: 1.691→1.751 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1633 / Mean I/σ(I) obs: 3.66 / Num. unique obs: 5380 / CC1/2: 0.932 / CC star: 0.982 / Rpim(I) all: 0.1633 / Rrim(I) all: 0.231 / % possible all: 82.82

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
pointlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.691→33.95 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2655 --
Rwork0.2294 --
obs-65768 91.45 %
Refinement stepCycle: LAST / Resolution: 1.691→33.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 73 190 4444

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