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- PDB-7kvy: Crystal Structure of Acetyl-CoA synthetase in complex with adenos... -

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Basic information

Entry
Database: PDB / ID: 7kvy
TitleCrystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate and Co-enzyme A from Coccidioides immitis RS
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Acetyl-coenzyme A synthetase / ethyl-AMP / CoA / Co-Enzyme A / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acetate-CoA ligase / acetyl-CoA synthetase activity / : / 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
COENZYME A / 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate and Co-enzyme A from Coccidioides immitis RS
Authors: Fox III, D. / Abendroth, J. / DeBouver, N.D. / Esan, T.E. / Hagen, T.J. / Krysan, D.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,13712
Polymers78,4361
Non-polymers1,70111
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.940, 106.940, 115.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 78435.828 Da / Num. of mol.: 1 / Fragment: CoimA.00629.a.FS11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (strain RS) (fungus)
Strain: RS / Gene: CIMG_01510 / Plasmid: CoimA.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3KJC6, acetate-CoA ligase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-WTA / 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine


Mass: 375.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N5O7P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.45 Å3/Da / Density % sol: 49.8 % / Mosaicity: 0.18 °
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Optimization conditions around RigakuReagents JCSG H3: 18.32@ PEG3,350, 0.2M Lithium acetate; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'- ...Details: Optimization conditions around RigakuReagents JCSG H3: 18.32@ PEG3,350, 0.2M Lithium acetate; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'-ethylphosphate + 1mM Co-EnzymeA; Cryo: 20% ethylene glycol; tray 317944f5, puck dzd7-5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 24, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 59143 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 33.21 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.29
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.09 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19RC4_4035refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KCP

7kcp


Resolution: 1.9→46.31 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 1990 3.37 %
Rwork0.163 --
obs0.164 59133 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 109 344 5317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075167
X-RAY DIFFRACTIONf_angle_d0.8277045
X-RAY DIFFRACTIONf_dihedral_angle_d13.6031816
X-RAY DIFFRACTIONf_chiral_restr0.055764
X-RAY DIFFRACTIONf_plane_restr0.007900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30911460.26024066X-RAY DIFFRACTION100
1.95-20.23961370.24184044X-RAY DIFFRACTION100
2-2.060.25421400.21424060X-RAY DIFFRACTION100
2.06-2.130.22761440.20234080X-RAY DIFFRACTION100
2.13-2.20.21321450.1914058X-RAY DIFFRACTION100
2.2-2.290.22121400.17844082X-RAY DIFFRACTION100
2.29-2.390.18031410.16174081X-RAY DIFFRACTION100
2.39-2.520.20491460.16964057X-RAY DIFFRACTION100
2.52-2.680.21491420.17374113X-RAY DIFFRACTION100
2.68-2.880.22951410.17064075X-RAY DIFFRACTION100
2.88-3.170.2011350.16764078X-RAY DIFFRACTION100
3.18-3.630.18751460.15584104X-RAY DIFFRACTION100
3.64-4.580.15221390.13334099X-RAY DIFFRACTION100
4.58-46.310.17711480.15174146X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3392-0.7072-0.05682.20550.77811.3273-0.301-0.44210.65840.55150.286-1.4045-0.22580.5228-0.07330.63550.0236-0.39890.58-0.07080.9182-14.310935.402818.4885
20.92-0.4819-0.09872.5659-0.34450.8453-0.0403-0.03970.09350.13580.0624-0.2898-0.0313-0.0767-0.01690.2366-0.0221-0.01530.2616-0.00360.1935-37.306739.75971.9654
31.0747-0.3457-0.24742.0539-0.38951.31970.05760.33660.1544-0.6351-0.0294-0.4412-0.0249-0.0331-0.03070.4097-0.01270.12260.3430.06150.2616-34.318244.5848-18.3288
41.3812-0.9909-0.06053.0288-0.13390.8572-0.0378-0.05690.39810.18440.0347-1.1579-0.12810.17330.00950.2228-0.0548-0.05310.2462-0.01760.5207-20.398542.94812.3183
52.9119-0.65670.74892.72040.49622.54090.01150.0734-0.19950.1650.0229-0.59770.31740.26-0.03480.27730.0027-0.00680.21460.02340.3587-20.135919.1091.5558
61.6986-0.23810.19742.5779-1.07362.88420.07060.25270.1233-0.37650.0069-1.06480.07970.3656-0.05060.37550.01290.1620.4398-0.03350.7859-10.380828.2864-10.498
72.02210.34390.39741.0241-0.74214.4120.34740.53870.095-0.4586-0.017-0.7375-0.231.1541-0.28080.6461-0.03240.36110.8635-0.0630.9698-4.680531.6588-24.8312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 10 THROUGH 52 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 53 THROUGH 160 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 161 THROUGH 259 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 260 THROUGH 453 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 454 THROUGH 516 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 517 THROUGH 569 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 570 THROUGH 668 )

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