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- PDB-7ei4: Crystal structure of MasL in complex with a novel covalent inhibi... -

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Basic information

Entry
Database: PDB / ID: 7ei4
TitleCrystal structure of MasL in complex with a novel covalent inhibitor, collimonin C
ComponentsAcetyl-CoA C-acyltransferase
KeywordsTRANSFERASE/INHIBITOR / Acetyl-CoA acetyltransferase / TRANSFERASE-INHIBITOR complex
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Chem-J3U / :
Function and homology information
Biological species[Empedobacter] haloabium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsLin, C.C. / Huang, K.F. / Yang, Y.L.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)MOST 104-2320-B-001-019-MY2 Taiwan
CitationJournal: Commun Biol / Year: 2022
Title: Integrated omics approach to unveil antifungal bacterial polyynes as acetyl-CoA acetyltransferase inhibitors.
Authors: Lin, C.C. / Hoo, S.Y. / Ma, L.T. / Lin, C. / Huang, K.F. / Ho, Y.N. / Sun, C.H. / Lee, H.J. / Chen, P.Y. / Shu, L.J. / Wang, B.W. / Hsu, W.C. / Ko, T.P. / Yang, Y.L.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-CoA C-acyltransferase
B: Acetyl-CoA C-acyltransferase
C: Acetyl-CoA C-acyltransferase
D: Acetyl-CoA C-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,5358
Polymers170,4294
Non-polymers1,1054
Water30,7701708
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14640 Å2
ΔGint-83 kcal/mol
Surface area49580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.139, 115.077, 125.789
Angle α, β, γ (deg.)90.000, 91.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetyl-CoA C-acyltransferase


Mass: 42607.332 Da / Num. of mol.: 4 / Mutation: V183T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Empedobacter] haloabium (bacteria) / Gene: E7V67_18950 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5C7BKK5, acetyl-CoA C-acyltransferase
#2: Chemical
ChemComp-J3U / (6S,7R,9E)-6,7-bis(oxidanyl)hexadeca-9,15-dien-11,13-diynoic acid


Mass: 276.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1708 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (w/v) polyethylene glycol 3,350 and 0.2 M tri-lithium citrate, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→30 Å / Num. obs: 197431 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.7
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / Num. unique obs: 18672 / % possible all: 94.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N44

4n44


Resolution: 1.66→29.22 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.752 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1617 9113 5 %RANDOM
Rwork0.1142 ---
obs0.1166 171828 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.95 Å2 / Biso mean: 18.347 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å2-0.09 Å2
2--0.09 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.66→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11428 0 80 1708 13216
Biso mean--44.01 33.9 -
Num. residues----1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01311812
X-RAY DIFFRACTIONr_bond_other_d0.0030.01711260
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.63816032
X-RAY DIFFRACTIONr_angle_other_deg1.5161.5825916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68651572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83921.293588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.412151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.75715100
X-RAY DIFFRACTIONr_chiral_restr0.0740.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022464
X-RAY DIFFRACTIONr_rigid_bond_restr1.4323072
LS refinement shellResolution: 1.66→1.701 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 498 -
Rwork0.178 8476 -
obs--61.16 %

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