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- PDB-7l3p: Crystal Structure of Acetyl-CoA synthetase in complex with adenos... -

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Basic information

Entry
Database: PDB / ID: 7l3p
TitleCrystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate and Co-enzyme A from Coccidioides immitis RS
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Acetyl-coenzyme A synthetase / methyl-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 / 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
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: 2.1 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,40411
Polymers78,4361
Non-polymers96810
Water5,350297
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)107.570, 107.570, 116.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.49 Å3/Da / Density % sol: 50.57 % / Mosaicity: 0.17 °
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: RigakuReagents MCSG-1, F11: 0.1M HEPES/NaOH, pH7.5, 0.2M Ammonium sulfate, 25% w/v PEG 3,350; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'- ...Details: RigakuReagents MCSG-1, F11: 0.1M HEPES/NaOH, pH7.5, 0.2M Ammonium sulfate, 25% w/v PEG 3,350; CoimA.00629.a.FS11.PD00401 at 10 mg/mL + 1mM TCEP (added first) + 1mM adenosine-5'-methylphosphate; Cryo: 15% ethylene glycol; tray 317937f11, puck mgf7-5.

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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: 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: 2.1→50 Å / Num. obs: 44619 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 36.93 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.95
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.72 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXV1.19RC4-4035refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KCP

7kcp


Resolution: 2.1→46.58 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 2006 4.5 %
Rwork0.16 --
obs0.161 44615 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 61 297 4942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074831
X-RAY DIFFRACTIONf_angle_d0.7946584
X-RAY DIFFRACTIONf_dihedral_angle_d13.3931692
X-RAY DIFFRACTIONf_chiral_restr0.055713
X-RAY DIFFRACTIONf_plane_restr0.007845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.2531480.22313033X-RAY DIFFRACTION100
2.15-2.210.25931390.1993040X-RAY DIFFRACTION100
2.21-2.280.23191450.18733019X-RAY DIFFRACTION100
2.28-2.350.20191370.17133042X-RAY DIFFRACTION100
2.35-2.430.22921470.1653027X-RAY DIFFRACTION100
2.43-2.530.19691400.17023025X-RAY DIFFRACTION100
2.53-2.650.20811430.17563056X-RAY DIFFRACTION100
2.65-2.780.21731430.18763044X-RAY DIFFRACTION100
2.79-2.960.26521420.16923029X-RAY DIFFRACTION100
2.96-3.190.20121400.17613040X-RAY DIFFRACTION100
3.19-3.510.18821430.16433046X-RAY DIFFRACTION100
3.51-4.020.18221480.13683052X-RAY DIFFRACTION100
4.02-5.060.14961480.1253054X-RAY DIFFRACTION100
5.06-46.580.18781430.16493102X-RAY DIFFRACTION100
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)
12.4958-0.8749-0.362.03520.05721.2831-0.01-0.031-0.5357-0.0354-0.00720.43810.0935-0.0278-0.01960.218-0.0407-0.00120.2168-0.00730.2827-18.635347.40881.6815
22.1535-0.7386-0.14491.76340.11060.85770.0560.0901-0.78-0.0191-0.06860.68960.1588-0.12720.0060.2596-0.0407-0.01310.2567-0.02580.5172-25.357939.89130.12
33.47021.16691.50273.46830.93842.42820.21980.0122-1.07370.175-0.06070.33760.4764-0.06-0.1680.31420.01530.0050.27710.00440.5924-10.197227.84091.2739
41.7181.9143-2.90483.8627-4.17665.77740.4208-0.472-0.2289-0.19890.01290.23510.8712-0.2987-0.25141.156-0.08960.02541.01580.34051.0459-23.34325.416526.4564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 236 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 237 THROUGH 483 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 484 THROUGH 541 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 542 THROUGH 616 )

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