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- PDB-8g0r: Crystal Structure of Acetyl-CoA synthetase in complex with a cycl... -

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Basic information

Entry
Database: PDB / ID: 8g0r
TitleCrystal Structure of Acetyl-CoA synthetase in complex with a cyclopentyl ester AMP inhibitor from Cryptococcus neoformans H99
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding / cytosol
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-YHF / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Acetyl-CoA synthetase in complex with a cyclopentyl ester AMP inhibitor from Cryptococcus neoformans H99
Authors: Lovell, S. / Liu, L. / Battaile, K.P. / Staker, B.L.
History
DepositionFeb 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,6736
Polymers232,4273
Non-polymers1,2463
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.922, 86.971, 105.190
Angle α, β, γ (deg.)66.31, 73.22, 89.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77475.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Plasmid: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A854QMN0
#2: Chemical ChemComp-YHF / 5'-O-[(S)-(cyclopentyloxy)(hydroxy)phosphoryl]adenosine


Mass: 415.338 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N5O7P / Feature type: SUBJECT OF INVESTIGATION
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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus H3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL- ...Details: Morpheus H3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine, CrneC.00629.a.FS11.PD00460 at 10 mg/mL. SCRI MorphH3 / HGN1192, Puck: CPS5110 position 14, Cryo: Direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 30, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→49.56 Å / Num. obs: 58184 / % possible obs: 97.4 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.062 / Rrim(I) all: 0.112 / Χ2: 0.95 / Net I/σ(I): 8.1 / Num. measured all: 180312
Reflection shellResolution: 2.6→2.67 Å / % possible obs: 97.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.604 / Num. measured all: 13918 / Num. unique obs: 4516 / CC1/2: 0.765 / Rpim(I) all: 0.408 / Rrim(I) all: 0.731 / Χ2: 0.85 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→25.67 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 2888 4.98 %
Rwork0.2052 --
obs0.2077 58036 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14880 0 84 0 14964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315381
X-RAY DIFFRACTIONf_angle_d0.58821002
X-RAY DIFFRACTIONf_dihedral_angle_d11.3075471
X-RAY DIFFRACTIONf_chiral_restr0.0452307
X-RAY DIFFRACTIONf_plane_restr0.0052697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.34011560.27262639X-RAY DIFFRACTION97
2.64-2.690.33821600.26662584X-RAY DIFFRACTION98
2.69-2.740.35821410.26612650X-RAY DIFFRACTION97
2.74-2.790.33541460.26712619X-RAY DIFFRACTION97
2.79-2.850.31871390.24692619X-RAY DIFFRACTION97
2.85-2.910.33981510.25112617X-RAY DIFFRACTION97
2.91-2.980.31021190.25272651X-RAY DIFFRACTION98
2.98-3.050.3061500.25432619X-RAY DIFFRACTION98
3.05-3.130.32691340.25082652X-RAY DIFFRACTION97
3.13-3.220.3173960.23472683X-RAY DIFFRACTION97
3.22-3.330.30941480.22342627X-RAY DIFFRACTION98
3.33-3.450.28561290.22972637X-RAY DIFFRACTION97
3.45-3.580.24471260.22832619X-RAY DIFFRACTION97
3.58-3.750.2691580.20762628X-RAY DIFFRACTION97
3.75-3.940.26121350.20032647X-RAY DIFFRACTION97
3.94-4.190.2611130.18562636X-RAY DIFFRACTION97
4.19-4.510.2334960.17262634X-RAY DIFFRACTION97
4.51-4.960.18981760.15322575X-RAY DIFFRACTION97
4.96-5.670.22131140.17692616X-RAY DIFFRACTION96
5.67-7.120.24251740.19912582X-RAY DIFFRACTION97
7.13-25.670.17711270.16822614X-RAY DIFFRACTION97

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