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- PDB-7kds: Crystal structure of Acetyl-CoA synthetase 2 in complex with Aden... -

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Basic information

Entry
Database: PDB / ID: 7kds
TitleCrystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-propylphosphate from Candida albicans
ComponentsAcetyl-coenzyme A synthetase 2
KeywordsLIGASE / SSGCID / ACS2 / Acetate--CoA ligase 2 / Acyl-activating enzyme 2 / 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 / 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-5'-MONOPHOSPHATE-PROPYL ESTER / Acetyl-coenzyme A synthetase 2
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of Acetyl-CoA synthetase 2 in complex with Adenosine-5'-propylphosphate from Candida albicans
Authors: Abendroth, J. / Fox III, D. / DeBouver, N.D. / Krysan, D.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3213
Polymers75,9081
Non-polymers4122
Water724
1
A: Acetyl-coenzyme A synthetase 2
hetero molecules

A: Acetyl-coenzyme A synthetase 2
hetero molecules

A: Acetyl-coenzyme A synthetase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,9629
Polymers227,7253
Non-polymers1,2376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area6210 Å2
ΔGint-23 kcal/mol
Surface area66250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.920, 166.920, 166.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-701-

NA

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Components

#1: Protein Acetyl-coenzyme A synthetase 2 / Acetate--CoA ligase 2 / Acyl-activating enzyme 2


Mass: 75908.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ACS2, CAALFM_C104290CA, CaO19.1064, CaO19.8666 / Plasmid: CaalA.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NJN3, acetate-CoA ligase
#2: Chemical ChemComp-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE


Mass: 389.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytics MCSG1 screen, condition G10: 100mM Mg-formate, 15% (wV) PEG 3350: CaalA.00629.a.FS11.PD00399 at 10mg/ml + 1mM Propyl-AMP + 1mM TCEP: tray: 313278g10: cryo: 25% EG + compounds: puck cfh0-10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2020 / Details: DCM, Si-111
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 18239 / % possible obs: 99.9 % / Redundancy: 38.471 % / Biso Wilson estimate: 104.656 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.082 / Χ2: 0.855 / Net I/σ(I): 34.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.9835.1622.6171.5513050.6342.655100
2.98-3.0639.1211.9452.3412760.8381.97100
3.06-3.1540.6431.443.3512650.8791.458100
3.15-3.2440.2170.955.1811970.9570.962100
3.24-3.3538.5810.6447.6311800.9750.652100
3.35-3.4739.720.45510.7511480.990.461100
3.47-3.638.6540.32114.8211000.9940.326100
3.6-3.7440.5230.22821.1610740.9970.23100
3.74-3.9139.870.17227.2310180.9980.174100
3.91-4.138.170.1236.89910.9990.122100
4.1-4.3239.0230.0948.029380.9990.092100
4.32-4.5938.2990.07256.5288710.072100
4.59-4.939.4420.06166.9785710.062100
4.9-5.2938.190.05966.9378410.06100
5.29-5.837.8230.05769.5973610.058100
5.8-6.4837.8640.0575.6866910.05100
6.48-7.4937.4220.04385.3960910.044100
7.49-9.1734.8240.036102.2651810.036100
9.17-12.9734.8310.031116.7242510.032100
12.97-5029.0760.032107.4726210.03396

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc2refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5ifi

5ifi


Resolution: 2.9→48.19 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 1881 10.34 %
Rwork0.2319 16307 -
obs0.2355 18188 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.22 Å2 / Biso mean: 118.4022 Å2 / Biso min: 74.89 Å2
Refinement stepCycle: final / Resolution: 2.9→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 27 4 4832
Biso mean--111.65 99.77 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034954
X-RAY DIFFRACTIONf_angle_d0.4936785
X-RAY DIFFRACTIONf_dihedral_angle_d11.831675
X-RAY DIFFRACTIONf_chiral_restr0.042762
X-RAY DIFFRACTIONf_plane_restr0.005899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-2.980.34611220.354212531375
2.98-3.070.38721390.323112121351
3.07-3.170.34971530.318812181371
3.17-3.280.4021450.348512291374
3.28-3.410.36261390.312312211360
3.41-3.570.331200.279212581378
3.57-3.750.33741460.258912251371
3.75-3.990.29551480.257712411389
3.99-4.30.27481400.226612571397
4.3-4.730.231570.181712511408
4.73-5.410.23811240.213212891413
5.42-6.810.25261730.227312741447
6.83-48.190.2271750.207213791554
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)
11.9036-0.29660.44182.56450.63383.5055-0.1661-0.1675-0.02520.0305-0.10070.3533-0.4062-0.47630.30320.76630.0326-0.00030.78540.00010.763322.2599-27.9957-30.1901
20.9010.62510.50142.8221.33221.545-0.1236-0.20210.62630.1439-0.23170.4603-0.4982-0.52430.31030.96940.1897-0.06061.1073-0.16161.060925.7687-11.4706-15.8385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 370 )A20 - 370
2X-RAY DIFFRACTION2chain 'A' and (resid 371 through 683 )A371 - 683

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