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- PDB-7l3q: Crystal Structure of Acetyl-CoA synthetase in complex with adenos... -

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Basic information

Entry
Database: PDB / ID: 7l3q
TitleCrystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-methylphosphate and Co-enzyme A from Coccidioides immitis RS
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Acetyl-coenzyme A synthetase / methyl-AMP / CoA / Co-Enzyme A / 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
COENZYME A / 5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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'-methylphosphate 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
DepositionDec 18, 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
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,68725
Polymers235,3073
Non-polymers4,37922
Water9,728540
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9379
Polymers78,4361
Non-polymers1,5018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9379
Polymers78,4361
Non-polymers1,5018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8137
Polymers78,4361
Non-polymers1,3776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.440, 116.270, 106.820
Angle α, β, γ (deg.)90.00, 119.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 78435.828 Da / Num. of mol.: 3 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-XM7 / 5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine


Mass: 361.248 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H16N5O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 49.73 % / Mosaicity: 0.25 °
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: RigakuReagents MCSG-1, A6: 18.71% PEG 3,350, 0.2M Lithium acetate; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'-methylphosphate + 1mM Co-Enyzme A; Cryo: ...Details: RigakuReagents MCSG-1, A6: 18.71% PEG 3,350, 0.2M Lithium acetate; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'-methylphosphate + 1mM Co-Enyzme A; Cryo: 20% ethylene glycol; tray 317940a6, puck mgf7-8.

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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: 2.15→50 Å / Num. obs: 115434 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 38.24 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.74
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.24 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.19RC4-4035refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KCP

7kcp


Resolution: 2.15→46.38 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2058 1.78 %
Rwork0.187 --
obs0.188 115426 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.53 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14395 0 280 540 15215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715134
X-RAY DIFFRACTIONf_angle_d0.84420651
X-RAY DIFFRACTIONf_dihedral_angle_d13.9315220
X-RAY DIFFRACTIONf_chiral_restr0.0562245
X-RAY DIFFRACTIONf_plane_restr0.0072646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.33741470.27937781X-RAY DIFFRACTION97
2.2-2.260.30781320.26667818X-RAY DIFFRACTION97
2.26-2.320.28571410.24827746X-RAY DIFFRACTION97
2.32-2.380.24251370.23357706X-RAY DIFFRACTION96
2.38-2.460.27981430.2217708X-RAY DIFFRACTION96
2.46-2.550.26231410.22557671X-RAY DIFFRACTION96
2.55-2.650.26441350.21367596X-RAY DIFFRACTION95
2.65-2.770.25361400.20937584X-RAY DIFFRACTION94
2.77-2.920.25451460.20767527X-RAY DIFFRACTION94
2.92-3.10.25931350.20437432X-RAY DIFFRACTION93
3.1-3.340.24091380.1957450X-RAY DIFFRACTION92
3.34-3.680.22891290.17777387X-RAY DIFFRACTION92
3.68-4.210.19611410.1547308X-RAY DIFFRACTION91
4.21-5.30.18191300.14567356X-RAY DIFFRACTION91
5.3-46.380.22421230.17297298X-RAY DIFFRACTION89
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)
12.69040.75550.66452.2650.34463.30740.1897-0.80870.48071.02840.10180.0739-0.2542-0.055-0.27840.79060.1130.06930.6478-0.29820.650610.880419.89851.9476
22.2098-0.11510.00191.3823-0.08391.28330.0343-0.5533-0.06890.234-0.0083-0.00990.0748-0.0456-0.0060.33550.0069-0.01820.29360.02230.209922.3171-0.829742.9423
33.05210.2151-0.21672.47340.54563.34050.0227-0.46910.13380.2937-0.02960.3599-0.064-0.57930.02520.33110.00270.05680.41740.02430.31841.94650.561641.4043
41.9480.0139-0.5513.0714-3.17313.43510.0486-0.2393-0.05220.9874-0.10510.3024-0.11570.18620.03491.008-0.1590.17930.75170.24070.86574.0788-21.546453.922
51.69990.2132-0.44880.16020.30531.88290.2003-0.9477-0.50761.4636-0.11980.4683-0.11140.0816-0.03891.11-0.16710.28130.70470.280.88143.3504-23.625958.3205
63.4805-0.61690.63882.86290.14913.00240.07040.49630.418-0.6240.03010.6724-0.6722-0.7211-0.04970.57160.114-0.10870.58940.26210.64093.32519.89-16.1811
71.82640.0103-0.47280.92620.0671.5091-0.03870.1857-0.23420.0692-0.00270.04450.1929-0.20160.03220.2492-0.0547-0.01610.21440.00760.30458.3758-6.16726.0141
81.0823-0.1146-0.53250.99290.01821.6833-0.01750.45360.0169-0.0890.0250.2847-0.0089-0.5960.00310.2399-0.0386-0.05110.42430.03680.32580.02611.8412-4.1448
91.447-0.2055-0.09811.7238-0.0821.8324-0.00240.57550.2238-0.26930.07610.09710.0062-0.4819-0.06020.3184-0.0466-0.0640.48030.09080.297311.03185.8659-18.2206
101.60720.38410.01337.44350.50372.1050.10480.9727-0.2975-0.605-0.1440.47630.3938-0.14660.03390.5565-0.0657-0.12170.8131-0.15270.56137.5728-9.1539-23.2163
111.67020.42411.02430.6885-0.73462.3814-0.16980.4335-0.1436-0.9799-0.31920.98780.5511-0.75990.38620.9393-0.1276-0.20550.8165-0.32070.95711.3144-23.4665-26.2639
123.0560.1823-0.18512.4895-0.03412.3075-0.22920.43270.635-0.363-0.0096-0.6546-0.58841.0710.2390.5354-0.22010.00080.68690.11240.634466.185419.620110.9454
131.4077-0.20320.18651.0904-0.40351.69150.01280.1635-0.1556-0.1755-0.0293-0.0290.36750.23350.00970.31110.05280.03670.2103-0.03750.2644.0238-6.1994.3472
141.29740.03980.56170.9524-0.02371.9186-0.00310.1570.0804-0.1004-0.0255-0.23520.02760.69010.02630.23560.03550.06020.3841-0.00460.328359.84083.50049.2023
151.03970.65250.29178.14960.41631.3569-0.0111-0.0495-0.6121-0.0934-0.015-1.25070.40990.69510.04310.460.18860.08350.70770.00930.715969.514-9.585318.0172
163.7318-2.4352-0.70471.97781.28461.88550.25670.5731-0.1272-0.3716-0.2078-1.1387-0.08740.1318-0.04070.71410.33890.23050.7760.08721.134272.7663-26.239811.4863
172.2482-1.08720.84022.03021.43553.05670.02960.34670.5282-0.08830.0851-1.12150.0171.136-0.14030.54260.1780.13970.89430.09441.278978.4609-20.506616.3414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'C' AND (RESID 11 THROUGH 53 )
2X-RAY DIFFRACTION2CHAIN 'C' AND (RESID 54 THROUGH 484 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 485 THROUGH 542 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 543 THROUGH 589 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 590 THROUGH 669 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 10 THROUGH 53 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 54 THROUGH 260 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 261 THROUGH 407 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 408 THROUGH 517 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 518 THROUGH 570 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 571 THROUGH 669 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 10 THROUGH 53 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 54 THROUGH 260 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 261 THROUGH 517 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 518 THROUGH 570 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 571 THROUGH 604 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 605 THROUGH 669 )

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