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- PDB-8u2u: Crystal Structure of Acetyl-coenzyme A synthetase from Leishmania... -

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Basic information

Entry
Database: PDB / ID: 8u2u
TitleCrystal Structure of Acetyl-coenzyme A synthetase from Leishmania infantum (CoA, AMP and potassium bound)
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Acetyl-coenzyme A synthetase
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / mitochondrion / 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 / 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, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / COENZYME A / : / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Acetyl-coenzyme A synthetase from Leishmania infantum (CoA, AMP and potassium bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionSep 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6957
Polymers79,3781
Non-polymers1,3176
Water3,999222
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)58.752, 69.465, 149.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetyl-coenzyme A synthetase / 2 / 3-dihydro-2 / 3-dihydroxybenzoate dehydrogenase


Mass: 79377.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINJ_23_0580 / Plasmid: LeinA.00629.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4I093

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ G10: 30% PEG 2000MME, 150 mM KBr. LeinA.00629.b.B1.PW39174 at 20 mg/mL. Plate 13159 well G10 drop 2. Puck: PSL-0106, Cryo: Direct. 2mM CoA and AMP added prior to crystallization. ...Details: JCSG+ G10: 30% PEG 2000MME, 150 mM KBr. LeinA.00629.b.B1.PW39174 at 20 mg/mL. Plate 13159 well G10 drop 2. Puck: PSL-0106, Cryo: Direct. 2mM CoA and AMP added prior to crystallization. Potassium binding near the AMP was confirmed with another data set obtained from crystals with 100mM KSCN in the crystallant (JCSG+ G9).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→74.69 Å / Num. obs: 44111 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 13.5
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.614 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3226 / CC1/2: 0.873 / Rpim(I) all: 0.475 / Rrim(I) all: 1.684 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40.47 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 2196 5.01 %
Rwork0.1629 --
obs0.1656 43855 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5156 0 63 222 5441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125397
X-RAY DIFFRACTIONf_angle_d1.0087361
X-RAY DIFFRACTIONf_dihedral_angle_d13.5631940
X-RAY DIFFRACTIONf_chiral_restr0.06799
X-RAY DIFFRACTIONf_plane_restr0.01938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.27511440.25782556X-RAY DIFFRACTION99
2.01-2.060.28331340.24212565X-RAY DIFFRACTION99
2.06-2.110.31621380.21962547X-RAY DIFFRACTION99
2.11-2.170.27981220.20092583X-RAY DIFFRACTION99
2.17-2.230.24671290.18382539X-RAY DIFFRACTION99
2.23-2.30.24971390.1742573X-RAY DIFFRACTION99
2.3-2.390.23661180.16862583X-RAY DIFFRACTION99
2.39-2.480.23751310.16312584X-RAY DIFFRACTION99
2.48-2.590.23031360.16782585X-RAY DIFFRACTION99
2.59-2.730.2121190.1622615X-RAY DIFFRACTION100
2.73-2.90.19511380.1612607X-RAY DIFFRACTION100
2.9-3.130.21631360.17962615X-RAY DIFFRACTION100
3.13-3.440.21761550.16412614X-RAY DIFFRACTION100
3.44-3.940.22711680.14812624X-RAY DIFFRACTION100
3.94-4.960.17371320.12782681X-RAY DIFFRACTION100
4.96-40.470.19971570.16552788X-RAY DIFFRACTION99
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)
14.20031.41480.62982.9020.44782.5975-0.0537-0.4260.14890.136-0.01330.2209-0.1888-0.21020.07140.31110.01270.04320.4575-0.03060.277-35.2021.82234.026
21.78690.04060.02680.9260.17150.93980.0441-0.1828-0.18930.0257-0.022-0.10640.02860.1225-0.02460.2504-0.008-0.03380.36740.04830.3317-9.218-7.01822.193
35.41631.0999-1.00524.9303-2.59785.21110.0311-0.1541-0.7558-0.0273-0.1235-0.38270.29480.60870.08980.30660.0644-0.01560.4874-0.04110.56322.969-17.72216.048
42.27020.8210.16231.51540.31810.86170.0098-0.0921-0.1532-0.07630.0118-0.09280.0158-0.0661-0.01420.26080.01920.0010.31040.04170.2669-25.561-10.05419.274
54.38611.7610.02152.8601-0.66311.2429-0.0543-0.07470.3617-0.08250.01560.1404-0.2334-0.06680.03310.3230.0299-0.00640.2914-0.02220.2506-27.21710.69319.853
63.8331-0.8414-3.5920.55321.28644.0302-0.02320.0480.2618-0.10350.0933-0.1093-0.00050.0308-0.06980.40370.0141-0.01020.38260.07980.3632-25.165.9633.204
73.1878-0.9093-0.00364.5373-0.37942.39010.0790.52030.2209-0.414-0.0666-0.1521-0.06420.0949-0.00550.31-0.02640.00790.34380.03160.2645-19.4692.155-11.38
83.97810.6618-0.08617.835-0.30371.9844-0.060.04390.11330.04650.12720.0697-0.1472-0.1417-0.0690.49440.0407-0.03060.55690.11890.539-30.82611.083-13.749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 48:93 )A48 - 93
2X-RAY DIFFRACTION2( CHAIN A AND RESID 94:265 )A94 - 265
3X-RAY DIFFRACTION3( CHAIN A AND RESID 266:305 )A266 - 305
4X-RAY DIFFRACTION4( CHAIN A AND RESID 306:467 )A306 - 467
5X-RAY DIFFRACTION5( CHAIN A AND RESID 468:559 )A468 - 559
6X-RAY DIFFRACTION6( CHAIN A AND RESID 560:612 )A560 - 612
7X-RAY DIFFRACTION7( CHAIN A AND RESID 613:672 )A613 - 672
8X-RAY DIFFRACTION8( CHAIN A AND RESID 673:702 )A673 - 702

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