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

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Basic information

Entry
Database: PDB / ID: 7kqz
TitleCrystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Coccidioides immitis RS
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Acetyl-coenzyme A synthetase / ethyl-AMP / 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
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: 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'-ethylphosphate 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 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1217
Polymers78,4361
Non-polymers6866
Water5,765320
1
A: Acetyl-coenzyme A synthetase
hetero molecules

A: Acetyl-coenzyme A synthetase
hetero molecules

A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,36421
Polymers235,3073
Non-polymers2,05718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7460 Å2
ΔGint20 kcal/mol
Surface area61320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.200, 107.200, 116.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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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-WTA / 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine


Mass: 375.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Optimization condition around Molecular Dimensions MCSG1 H3: 200mM lithium acetate, 19.1% PEG 3350: CoimA.00629.a.FS11.PD00401 at 10mg/ml + 1mM TCEP + 1mM ethylAMP: tray 317942 F7: cryo: 20% ...Details: Optimization condition around Molecular Dimensions MCSG1 H3: 200mM lithium acetate, 19.1% PEG 3350: CoimA.00629.a.FS11.PD00401 at 10mg/ml + 1mM TCEP + 1mM ethylAMP: tray 317942 F7: cryo: 20% EG + ligands: puck FBB2-2.

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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: Oct 1, 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: 41174 / % possible obs: 100 % / Redundancy: 9.423 % / Biso Wilson estimate: 42.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.071 / Χ2: 0.939 / Net I/σ(I): 21.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.219.5530.5574.2430160.9030.589100
2.21-2.279.5590.4655.1329640.9330.492100
2.27-2.339.5520.3666.5228800.9610.387100
2.33-2.49.5630.298.2327940.9730.306100
2.4-2.489.570.2469.5427100.9790.26100
2.48-2.579.570.21211.0426070.9850.224100
2.57-2.679.5580.17812.8625410.9890.189100
2.67-2.789.5320.14715.6624510.9920.156100
2.78-2.99.4750.11619.3823250.9950.122100
2.9-3.049.4220.09523.3322350.9960.1100
3.04-3.219.3860.07827.4121160.9970.082100
3.21-3.49.2840.06233.1220030.9980.065100
3.4-3.639.1530.05337.6419150.9980.057100
3.63-3.939.1420.04642.3617550.9990.049100
3.93-4.39.1160.04146.216460.9990.043100
4.3-4.819.1890.03749.0814630.9990.039100
4.81-5.559.2580.03648.9813010.9990.038100
5.55-6.89.2750.03448.7411080.9990.036100
6.8-9.629.2960.02951.7486110.031100
9.62-508.650.02752.44830.9990.02998.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5ifi

5ifi


Resolution: 2.15→36.25 Å / SU ML: 0.2333 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1896 4.61 %0
Rwork0.1666 39246 --
obs0.1684 41142 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.75 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4701 0 45 320 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674886
X-RAY DIFFRACTIONf_angle_d0.78966662
X-RAY DIFFRACTIONf_chiral_restr0.0553723
X-RAY DIFFRACTIONf_plane_restr0.0078861
X-RAY DIFFRACTIONf_dihedral_angle_d13.19931684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.24311540.22662764X-RAY DIFFRACTION100
2.2-2.260.2678970.21242832X-RAY DIFFRACTION100
2.26-2.330.22551450.19572787X-RAY DIFFRACTION100
2.33-2.410.24791270.17462792X-RAY DIFFRACTION100
2.41-2.490.2341540.18382796X-RAY DIFFRACTION100
2.49-2.590.2066980.17892818X-RAY DIFFRACTION100
2.59-2.710.2391200.20182810X-RAY DIFFRACTION100
2.71-2.850.25011560.17252761X-RAY DIFFRACTION100
2.85-3.030.21061370.18382821X-RAY DIFFRACTION100
3.03-3.260.20211520.16922778X-RAY DIFFRACTION99.97
3.26-3.590.20441380.1672813X-RAY DIFFRACTION100
3.59-4.110.18691440.13882797X-RAY DIFFRACTION100
4.11-5.180.17291220.1362829X-RAY DIFFRACTION100
5.18-36.250.18961520.16992848X-RAY DIFFRACTION99.87
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)
11.837106826210.2217962739810.1083377290223.29650151772-0.0182964774291.727821858420.102931660546-0.195529432667-0.6943623112580.167304370508-0.102083220394-0.2279153829680.453068935674-0.2205612627840.002186026283150.312043565096-0.0434815480553-0.009712068344840.2606460159450.03504102833210.4068999101466.9196848816327.16456468481.74700959758
21.28855722313-0.4437709834230.7225755847851.72623062497-0.1282327927648.236875656150.2928388132210.534960870343-0.940193158348-0.6250333501950.121642420864-0.6146137887780.4897447541281.14449623221-0.6122233912470.740432276217-0.03732553742260.02533366608260.649962657026-0.1820902295120.94542883178519.524501261723.3868762535-10.2557161626
34.48100460235-2.172898648050.06637498926153.01895765691-0.8850704529360.3897979702210.2824731532330.192431618763-0.632814550525-0.1625429435130.370787990863-1.04325044430.5273577410820.550042096085-0.2573757055311.206754310770.127789971680.07537303862050.799052260254-0.3570689350.89204427089325.555696655122.6124383821-25.3194302457
42.092409147430.939751087517-0.3543307986532.33732772086-0.09437951194631.12547859341-0.004377401350680.0974731147887-0.437606551659-0.0106694637460.0251352598049-0.5264188799860.0744392799350.00287038645493-0.06332006704040.2330121615680.03554664153890.003001684149920.229486172869-0.01320422027850.26110280719319.041728834649.4921723028-3.09326595072
51.631520330470.769856685345-0.3136601811592.34455939978-0.0226975623980.6460112613220.0910219452878-0.142538819527-0.7667488434750.133345524712-0.082360072691-1.062714834590.170475425860.1442491490930.00309696681370.2918806957550.0426438544875-0.08770857186460.2725873966570.0519281464560.70110156850728.086514527938.1544327142.55019412222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 455 through 517 )455 - 517445 - 507
22chain 'A' and (resid 518 through 570 )518 - 570508 - 560
33chain 'A' and (resid 571 through 637 )571 - 637561 - 618
44chain 'A' and (resid 11 through 270 )11 - 2701 - 260
55chain 'A' and (resid 271 through 454 )271 - 454261 - 444

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