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- PDB-6l2c: Crystal structure of Aspergillus fumigatus mitochondrial acetyl-C... -

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Basic information

Entry
Database: PDB / ID: 6l2c
TitleCrystal structure of Aspergillus fumigatus mitochondrial acetyl-CoA acetyltransferase in complex with CoA
ComponentsAcetyl-CoA-acetyltransferase, putative
KeywordsTRANSFERASE / Aspergillus fumigatus / acetyl-CoA acetyltransferase
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase activity / acetyl-CoA C-acetyltransferase / mitochondrion / metal ion binding
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acetyl-CoA acetyltransferase erg10A, mitochondrial
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsZhang, Y. / Wei, W. / Raimi, O.G. / Ferenbach, A.T. / Fang, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31960032 China
National Natural Science Foundation of China31900404 China
CitationJournal: Appl.Environ.Microbiol. / Year: 2020
Title: Aspergillus fumigatus Mitochondrial Acetyl Coenzyme A Acetyltransferase as an Antifungal Target.
Authors: Zhang, Y. / Wei, W. / Fan, J. / Jin, C. / Lu, L. / Fang, W.
History
DepositionOct 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-CoA-acetyltransferase, putative
B: Acetyl-CoA-acetyltransferase, putative
C: Acetyl-CoA-acetyltransferase, putative
D: Acetyl-CoA-acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,8158
Polymers169,7454
Non-polymers3,0704
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19350 Å2
ΔGint-56 kcal/mol
Surface area52020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.254, 173.546, 180.318
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acetyl-CoA-acetyltransferase, putative


Mass: 42436.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus A1163 (mold) / Strain: A1163 / Gene: AFUB_000550 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: B0XMC1
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.44→49.67 Å / Num. obs: 74187 / % possible obs: 99.2 % / Redundancy: 3.59 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.9
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.072 / Num. unique obs: 74187

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F2S

2f2s


Resolution: 2.44→49.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 3736 5 %RANDOM
Rwork0.2034 ---
obs0.2061 70451 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.06 Å2 / Biso mean: 51.41 Å2 / Biso min: 24.94 Å2
Baniso -1Baniso -2Baniso -3
1-4.76 Å20 Å20 Å2
2---1.53 Å20 Å2
3----3.23 Å2
Refinement stepCycle: final / Resolution: 2.44→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11837 0 192 231 12260
Biso mean--94.5 41.85 -
Num. residues----1597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01312221
X-RAY DIFFRACTIONr_bond_other_d0.0360.01711562
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.6416584
X-RAY DIFFRACTIONr_angle_other_deg2.3931.57226824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11751593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.07323.165556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.619152015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4031564
X-RAY DIFFRACTIONr_chiral_restr0.120.21637
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213795
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022337
X-RAY DIFFRACTIONr_mcbond_it3.8175.2716384
X-RAY DIFFRACTIONr_mcbond_other3.8165.2716383
X-RAY DIFFRACTIONr_mcangle_it5.7477.8997973
LS refinement shellResolution: 2.44→2.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 270 -
Rwork0.339 4999 -
all-5269 -
obs--96.82 %

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