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- PDB-9mqf: Chloroplast acyl-ACP thioesterase from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 9mqf
TitleChloroplast acyl-ACP thioesterase from Chlamydomonas reinhardtii
ComponentsAcyl-[acyl-carrier-protein] hydrolase
KeywordsHYDROLASE / Thioesterase / Fatty Acid Biosynthesis / Chloroplast
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Thioester hydrolases / fatty acyl-[ACP] hydrolase activity / acyl carrier activity / chloroplast
Similarity search - Function
Acyl-ACP thioesterase / Acyl-[acyl-carrier-protein] hydrolase FATA/B / : / Acyl-ACP thioesterase N-terminal domain / Acyl-ACP thioesterase C-terminal domain / HotDog domain superfamily
Similarity search - Domain/homology
Acyl-[acyl-carrier-protein] hydrolase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, J.A. / Suo, Y. / Mayfield, S.P. / Burkart, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2011924 United States
CitationJournal: Biochemistry / Year: 2025
Title: Structural Characterization of an Endogenous Algal Acyl-ACP Thioesterase.
Authors: Chen, J.A. / Suo, Y. / Mayfield, S.P. / Burkart, M.D.
History
DepositionJan 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein] hydrolase


Theoretical massNumber of molelcules
Total (without water)39,0011
Polymers39,0011
Non-polymers00
Water1448
1
A: Acyl-[acyl-carrier-protein] hydrolase

A: Acyl-[acyl-carrier-protein] hydrolase


Theoretical massNumber of molelcules
Total (without water)78,0022
Polymers78,0022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area3210 Å2
ΔGint-2 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.259, 67.259, 207.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Acyl-[acyl-carrier-protein] hydrolase


Mass: 39000.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_06g256750v5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A8HY17, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3M sodium acetate, 1:2 protein:well solution ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.5→48.2 Å / Num. obs: 17356 / % possible obs: 100 % / Redundancy: 24.8 % / CC1/2: 1 / Net I/σ(I): 28.8
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 1873 / CC1/2: 0.903 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
REFMAC5refinement
HKL-20000.95data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.2 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.25 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.253 850 4.92 %
Rwork0.2372 --
obs0.238 17292 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 0 8 2299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032343
X-RAY DIFFRACTIONf_angle_d0.5573174
X-RAY DIFFRACTIONf_dihedral_angle_d13.793885
X-RAY DIFFRACTIONf_chiral_restr0.039346
X-RAY DIFFRACTIONf_plane_restr0.006414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.35581350.3182650X-RAY DIFFRACTION100
2.66-2.860.32661450.31082658X-RAY DIFFRACTION100
2.86-3.150.30791400.26412697X-RAY DIFFRACTION100
3.15-3.610.29181540.25592711X-RAY DIFFRACTION100
3.61-4.540.22171420.21952770X-RAY DIFFRACTION100
4.54-48.20.21811340.21682956X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 23.462 Å / Origin y: -12.667 Å / Origin z: 12.397 Å
111213212223313233
T0.4478 Å2-0.0431 Å20.0503 Å2-0.5272 Å20.026 Å2--0.5192 Å2
L4.2391 °2-1.1606 °2-0.913 °2-2.1818 °2-0.3028 °2--3.516 °2
S0.0118 Å °0.1316 Å °-0.3805 Å °0.0758 Å °-0.0718 Å °-0.13 Å °-0.0427 Å °0.1788 Å °0.0282 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 86:307 )

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