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- PDB-7kdn: Crystal structure of Acetyl-CoA Synthetase in Complex with Adenos... -

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Basic information

Entry
Database: PDB / ID: 7kdn
TitleCrystal structure of Acetyl-CoA Synthetase in Complex with Adenosine-5'-propylphosphate from Aspergillus fumigatus
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Aspergillus fumigatus / Acetyl CoenzymeA Synthetase / 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
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
Similarity search - Domain/homology
ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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'-propylphosphate from Aspergillus fumigatus
Authors: Fox III, D. / Abendroth, J. / 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 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)461,38712
Polymers459,0516
Non-polymers2,3366
Water77543
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8982
Polymers76,5091
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8982
Polymers76,5091
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8982
Polymers76,5091
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8982
Polymers76,5091
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8982
Polymers76,5091
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8982
Polymers76,5091
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.790, 104.210, 125.650
Angle α, β, γ (deg.)68.150, 66.550, 62.220
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 22 through 26 or (resid 27...
21(chain B and (resid 22 through 30 or (resid 31...
31(chain D and (resid 22 through 49 or (resid 50...
41(chain E and (resid 22 through 31 or (resid 32...
51(chain F and (resid 22 through 35 or (resid 36...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 22 through 26 or (resid 27...A22 - 26
121(chain A and (resid 22 through 26 or (resid 27...A27 - 28
131(chain A and (resid 22 through 26 or (resid 27...A12 - 695
141(chain A and (resid 22 through 26 or (resid 27...A12 - 695
151(chain A and (resid 22 through 26 or (resid 27...A12 - 695
161(chain A and (resid 22 through 26 or (resid 27...A12 - 695
211(chain B and (resid 22 through 30 or (resid 31...B22 - 30
221(chain B and (resid 22 through 30 or (resid 31...B31 - 32
231(chain B and (resid 22 through 30 or (resid 31...B21 - 695
241(chain B and (resid 22 through 30 or (resid 31...B21 - 695
251(chain B and (resid 22 through 30 or (resid 31...B21 - 695
261(chain B and (resid 22 through 30 or (resid 31...B21 - 695
311(chain D and (resid 22 through 49 or (resid 50...D22 - 49
321(chain D and (resid 22 through 49 or (resid 50...D50
331(chain D and (resid 22 through 49 or (resid 50...D22 - 695
341(chain D and (resid 22 through 49 or (resid 50...D22 - 695
351(chain D and (resid 22 through 49 or (resid 50...D22 - 695
361(chain D and (resid 22 through 49 or (resid 50...D22 - 695
411(chain E and (resid 22 through 31 or (resid 32...E22 - 31
421(chain E and (resid 22 through 31 or (resid 32...E32
431(chain E and (resid 22 through 31 or (resid 32...E13 - 638
441(chain E and (resid 22 through 31 or (resid 32...E13 - 638
451(chain E and (resid 22 through 31 or (resid 32...E13 - 638
461(chain E and (resid 22 through 31 or (resid 32...E13 - 638
511(chain F and (resid 22 through 35 or (resid 36...F22 - 35
521(chain F and (resid 22 through 35 or (resid 36...F36
531(chain F and (resid 22 through 35 or (resid 36...F20 - 638
541(chain F and (resid 22 through 35 or (resid 36...F20 - 638
551(chain F and (resid 22 through 35 or (resid 36...F20 - 638
561(chain F and (resid 22 through 35 or (resid 36...F20 - 638

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Components

#1: Protein
Acetyl-coenzyme A synthetase


Mass: 76508.547 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G11080 / Plasmid: pEMB7013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4WQ02, acetate-CoA ligase
#2: Chemical
ChemComp-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE


Mass: 389.301 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H20N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.34 Å3/Da / Density % sol: 47.58 % / Mosaicity: 0.2 °
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: RigakuReagents Morpheus screen, g9:10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02M carboxylic acids (sodium formate, ammonium acetate, trisodium citrate,sodium potassium L-tartrate, sodium ...Details: RigakuReagents Morpheus screen, g9:10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02M carboxylic acids (sodium formate, ammonium acetate, trisodium citrate,sodium potassium L-tartrate, sodium oxamate, 0.1M bicine/Trizma base pH8.5; AsfuA.00629.a.FS11.PD00486 at 10 mg/ml, 1mM TCEP, 1mM BSI5663/Propyl-AMP; cryo: direct; tray 313288g9, puck ejj3-5

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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: Nov 14, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 100485 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 57.775 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.139 / Χ2: 0.88 / Net I/σ(I): 10.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.8740.9371.5774050.7031.08397.5
2.87-2.950.8211.8271930.7320.94997.6
2.95-3.040.6182.3970430.8470.71497.7
3.04-3.130.5062.9468270.8830.58497.7
3.13-3.230.3554.0266650.9460.41197.9
3.23-3.350.2844.9564100.9610.32997.9
3.35-3.470.2415.9262060.9710.27998
3.47-3.610.1937.0359460.9830.22398.1
3.61-3.780.1588.8756850.9850.18397.8
3.78-3.960.12510.4655150.9910.14498.4
3.96-4.170.08913.4152250.9950.10398.3
4.17-4.430.0815.2249100.9950.09398.7
4.43-4.730.06517.8846750.9970.07598.4
4.73-5.110.05919.4243070.9970.06898.7
5.11-5.60.06418.6739670.9960.07598.2
5.6-6.260.06219.3535880.9960.07198.6
6.26-7.230.05221.7631710.9970.0698.3
7.23-8.850.03628.5526770.9980.04298.1
8.85-12.520.02736.0220430.9990.03297.2
12.52-500.02736.6610270.9980.03288.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFI

5ifi


Resolution: 2.8→47.92 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 1999 1.99 %
Rwork0.2155 98432 -
obs0.2161 100431 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.45 Å2 / Biso mean: 65.7636 Å2 / Biso min: 35.89 Å2
Refinement stepCycle: final / Resolution: 2.8→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26431 0 156 43 26630
Biso mean--64.74 52.71 -
Num. residues----3499
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12549X-RAY DIFFRACTION5.987TORSIONAL
12B12549X-RAY DIFFRACTION5.987TORSIONAL
13D12549X-RAY DIFFRACTION5.987TORSIONAL
14E12549X-RAY DIFFRACTION5.987TORSIONAL
15F12549X-RAY DIFFRACTION5.987TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.47111370.3536983712098
2.87-2.950.42771440.34266979712398
2.95-3.030.36821420.31167046718898
3.03-3.130.32161490.29446989713898
3.13-3.240.28741460.27077078722498
3.24-3.370.2971400.25326997713798
3.37-3.530.28921390.23777031717098
3.53-3.710.27811490.24827095724498
3.71-3.950.25611440.216975711998
3.95-4.250.22041440.18547093723799
4.25-4.680.18361330.1627103723699
4.68-5.350.18671490.16377038718799
5.35-6.740.21431480.19117064721299
6.74-47.920.17221350.17816961709697
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)
10.46090.3734-0.3010.374-0.18360.24510.09690.10560.46570.11150.03820.8603-0.031-0.20340.00010.63150.0103-0.03370.6882-0.07280.8133-31.8868-0.386817.7261
21.7872-0.02990.23150.79420.29731.0350.04190.3603-0.0814-0.0584-0.00790.0058-0.05650.047600.42180.0447-0.03760.49360.00240.4463-10.0058-4.4303-6.4549
31.90330.0046-0.30570.96320.22850.73830.07280.2052-0.2503-0.0558-0.05440.14940.0137-0.0985-00.41020.0642-0.07480.5277-0.01570.5155-23.3939-8.0861-1.3921
40.65980.21220.29290.06680.09630.1291-0.1884-0.13591.34210.0214-0.1607-0.1251-0.5837-0.0319-0.00680.51210.017-0.00730.5549-0.02680.7414-31.837717.23877.705
50.75080.29680.25690.8148-0.28680.2946-0.07050.26530.6049-0.13560.06180.2527-0.0425-0.25980.00010.52480.0627-0.06920.56460.05180.817-25.988113.7387-1.182
60.0481-0.06580.00690.33710.20370.1607-0.00770.30260.4392-0.572-0.0566-0.01660.219-0.12530.00020.9954-0.0060.01061.08510.31750.5948-36.39087.63-23.3274
70.24380.0849-0.13890.0343-0.07760.17260.2994-0.32470.4512-0.2207-0.6135-0.1350.0124-0.2317-0.00520.8090.1384-0.15811.37530.1810.9644-38.46047.2062-24.3894
82.0749-0.3049-0.1110.8026-0.32290.62510.07780.3256-0.2843-0.0167-0.0387-0.080.0482-0.0541-00.42740.0624-0.01680.5004-0.11650.492926.0686-9.4971-1.4106
90.5602-0.1304-0.26560.5611-0.75241.49120.04290.53770.0061-0.2558-0.01330.2950.097-0.06480.00020.51580.1317-0.02280.684-0.11450.715425.127-3.6061-12.1366
101.90730.07930.02111.41-0.04620.79920.14610.1894-0.6293-0.0325-0.1069-0.09580.15990.057100.46950.0699-0.05260.4989-0.07130.711430.8352-23.83212.662
111.0027-0.0684-0.11440.48010.03970.05940.00680.7884-0.5453-0.7453-0.0348-0.12940.0538-0.31870.00091.12020.1133-0.14530.9537-0.25161.443227.8396-32.8598-15.7012
120.0850.15180.08020.32170.04630.1623-0.3625-0.2020.20780.44520.1126-0.67440.08460.1379-00.9205-0.0526-0.04830.70110.02610.74021.07448.478229.0939
131.35050.1874-0.39581.4084-0.1870.61950.0764-0.0360.00380.23420.0033-0.01790.085-0.05-00.5685-0.0733-0.05410.4142-0.00170.3741-10.628927.848451.2739
140.3645-0.1138-0.26690.4538-0.04510.81520.0111-0.33840.25380.2030.00810.37760.3276-0.05180.00010.693-0.05390.03240.5738-0.05770.6283-17.197829.004960.6539
151.46930.0352-0.14821.74930.11351.1457-0.0627-0.0203-0.11650.04670.0636-0.33090.23730.088700.5994-0.0064-0.06730.4459-0.020.57671.922115.873944.2383
162.1761.06770.52160.52430.25640.1258-0.00070.006-0.0249-0.0457-0.02470.0570.054-0.05150.00021.0278-0.2438-0.57441.23080.0171.203117.283117.627854.1498
170.88430.06230.33440.59950.13120.70220.01480.09540.2075-0.0803-0.0142-0.0281-0.07920.0533-00.48570.02290.04430.4630.06870.676611.155626.6422-0.4945
181.35340.12270.47271.31490.14880.89090.00640.11520.3186-0.09430.05180.0056-0.2296-0.0034-00.47610.03550.06130.4910.07990.765810.276135.6815-1.0874
190.75270.3753-0.06661.0101-0.07880.90330.05490.05730.4056-0.0285-0.0386-0.1578-0.16060.157200.5227-0.01950.07080.50640.05080.920930.128433.67256.5583
200.0037-0.00590.0231-0.00180.01380.23030.0270.37550.007-0.36490.1585-0.1343-0.09890.287-0.00010.965-0.13120.17910.9649-0.01011.076933.338741.8633-13.3739
210.5841-0.09170.06930.0326-0.10090.46090.23640.02630.74130.3367-0.1023-0.0559-0.409-0.12480.00010.7271-0.046-0.0190.5501-0.00030.7141-42.765-10.478229.7217
221.29750.0040.04561.2631-0.24640.84220.0709-0.17270.09930.3502-0.0553-0.0693-0.1185-0.0513-00.5459-0.0634-0.0070.426-0.04710.4926-47.426-31.557853.7589
231.18420.01280.36021.6577-0.61851.31080.0167-0.13380.08820.2704-0.1312-0.2667-0.2110.1209-0.00020.5255-0.0735-0.02380.4193-0.07170.6085-38.7278-24.279351.184
240.89040.17270.5990.4940.05891.3205-0.04230.10610.20040.0313-0.14140.3747-0.3425-0.149300.6205-0.01650.06350.4263-0.01280.7548-51.3143-9.024744.052
250.59470.4457-0.08230.50810.23940.45220.0915-0.76820.09080.45520.10610.0451-0.05980.125300.99110.07140.05751.03040.00720.8978-49.0616-3.395258.0005
260.174-0.0090.16320.0884-0.00420.1687-0.0901-0.1944-0.0492-0.1934-0.0545-0.4599-0.4366-0.3426-01.5792-0.03080.12430.9836-0.20981.0065-43.268-2.606170.857
270.7625-0.08580.0091.44660.1661.29780.0684-0.11570.17450.18780.03290.3057-0.0288-0.2028-00.5091-0.02770.11780.5942-0.0090.789319.9043-35.532150.2875
281.03380.38620.04351.00860.58111.31390.0039-0.00250.22340.0883-0.13310.7355-0.0833-0.472-00.4955-0.00770.05570.7267-01.06775.4942-35.174743.7783
290.54520.0634-0.31960.6248-0.17890.70390.10380.1010.01830.1391-0.04970.69480.1864-0.13300.6365-0.1187-0.00320.69090.06831.04827.2442-57.314342.6313
300.2386-0.0044-0.0876-0.0065-0.01330.13710.4145-0.2211-0.04850.42460.17310.06710.2471-0.3666-0.00011.0692-0.13320.01121.2120.12691.0687-3.7123-51.547257.5516
310.1046-0.12110.11590.1518-0.13120.1298-0.19660.5520.5078-0.09360.0058-0.73550.4882-0.39390.01250.9137-0.22620.30161.45340.23581.3401-6.4974-45.635868.8927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 54 )A12 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 238 )A55 - 238
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 455 )A239 - 455
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 485 )A456 - 485
5X-RAY DIFFRACTION5chain 'A' and (resid 486 through 543 )A486 - 543
6X-RAY DIFFRACTION6chain 'A' and (resid 544 through 590 )A544 - 590
7X-RAY DIFFRACTION7chain 'A' and (resid 591 through 638 )A591 - 638
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 238 )B21 - 238
9X-RAY DIFFRACTION9chain 'B' and (resid 239 through 296 )B239 - 296
10X-RAY DIFFRACTION10chain 'B' and (resid 297 through 518 )B297 - 518
11X-RAY DIFFRACTION11chain 'B' and (resid 519 through 616 )B519 - 616
12X-RAY DIFFRACTION12chain 'C' and (resid 16 through 41 )C16 - 41
13X-RAY DIFFRACTION13chain 'C' and (resid 42 through 238 )C42 - 238
14X-RAY DIFFRACTION14chain 'C' and (resid 239 through 289 )C239 - 289
15X-RAY DIFFRACTION15chain 'C' and (resid 290 through 533 )C290 - 533
16X-RAY DIFFRACTION16chain 'C' and (resid 534 through 535 )C534 - 535
17X-RAY DIFFRACTION17chain 'D' and (resid 22 through 238 )D22 - 238
18X-RAY DIFFRACTION18chain 'D' and (resid 239 through 408 )D239 - 408
19X-RAY DIFFRACTION19chain 'D' and (resid 409 through 518 )D409 - 518
20X-RAY DIFFRACTION20chain 'D' and (resid 519 through 638 )D519 - 638
21X-RAY DIFFRACTION21chain 'E' and (resid 13 through 54 )E13 - 54
22X-RAY DIFFRACTION22chain 'E' and (resid 55 through 238 )E55 - 238
23X-RAY DIFFRACTION23chain 'E' and (resid 239 through 408 )E239 - 408
24X-RAY DIFFRACTION24chain 'E' and (resid 409 through 518 )E409 - 518
25X-RAY DIFFRACTION25chain 'E' and (resid 519 through 571 )E519 - 571
26X-RAY DIFFRACTION26chain 'E' and (resid 572 through 638 )E572 - 638
27X-RAY DIFFRACTION27chain 'F' and (resid 20 through 271 )F20 - 271
28X-RAY DIFFRACTION28chain 'F' and (resid 272 through 444 )F272 - 444
29X-RAY DIFFRACTION29chain 'F' and (resid 445 through 518 )F445 - 518
30X-RAY DIFFRACTION30chain 'F' and (resid 519 through 594 )F519 - 594
31X-RAY DIFFRACTION31chain 'F' and (resid 595 through 638 )F595 - 638

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