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

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Basic information

Entry
Database: PDB / ID: 7kcp
TitleCrystal structure of Acetyl-CoA Synthetase in Complex with Adenosine-5'-propylphosphate from Coccidioides posadasii C735
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Coccidioides posadasii / 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 / metal ion 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
ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCoccidioides posadasii
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: to be published
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Abendroth, J. / DeBouver, N.D. / Krysan, D.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,58814
Polymers78,4921
Non-polymers1,09613
Water6,593366
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)107.170, 107.170, 116.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 78491.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides posadasii (strain C735) (fungus)
Strain: C735 / Gene: CPC735_049370 / Plasmid: pEMB7013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5PGB4, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 49.87 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RigakuReagents Morpheus screen, a6:10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M divalent cations (MgCl2, CaCl2), 0.1M MOPS/HEPES-Na pH7.5; CopoA.00629.a.FS11.PD00403 at 10 mg/ml, 1mM ...Details: RigakuReagents Morpheus screen, a6:10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M divalent cations (MgCl2, CaCl2), 0.1M MOPS/HEPES-Na pH7.5; CopoA.00629.a.FS11.PD00403 at 10 mg/ml, 1mM TCEP, 1mM BSI5663/Propyl-AMP; cryo: direct; tray 313285a6, puck ejj3-4

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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: 2.15→50 Å / Num. obs: 41158 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 38.244 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.085 / Χ2: 0.992 / Net I/σ(I): 20.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.210.5814.230250.9050.616100
2.21-2.270.4914.9929590.9290.521100
2.27-2.330.3946.1528730.9610.418100
2.33-2.40.3187.5227910.9680.337100
2.4-2.480.2788.527150.9740.295100
2.48-2.570.2429.6826110.9810.256100
2.57-2.670.20711.2625430.9840.219100
2.67-2.780.17113.4224430.9890.182100
2.78-2.90.13116.9623250.9930.139100
2.9-3.040.10420.5122400.9960.11100
3.04-3.210.08524.2121140.9970.09100
3.21-3.40.06629.919980.9980.07100
3.4-3.630.05535.0119160.9980.059100
3.63-3.930.04639.7317560.9990.049100
3.93-4.30.04243.3616380.9990.045100
4.3-4.810.03946.5314640.9980.041100
4.81-5.550.03945.8613020.9990.042100
5.55-6.80.04144.5411060.9990.043100
6.8-9.620.03749.418580.9990.04100
9.62-500.03652.454810.9980.03999

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Processing

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

5ifi


Resolution: 2.15→36.26 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 1988 4.83 %
Rwork0.1538 39157 -
obs0.1556 41145 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.1 Å2 / Biso mean: 42.8062 Å2 / Biso min: 14.72 Å2
Refinement stepCycle: final / Resolution: 2.15→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 71 371 5011
Biso mean--40.96 41.21 -
Num. residues----594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.20.25111400.197527802920
2.2-2.260.2491460.185127872933
2.26-2.330.19181420.175227882930
2.33-2.410.22481440.165927682912
2.41-2.490.23181420.163128142956
2.49-2.590.24181420.162627742916
2.59-2.710.20571450.163527782923
2.71-2.850.19461420.166227802922
2.85-3.030.191390.159528202959
3.03-3.260.20431370.15927972934
3.26-3.590.16691380.146128142952
3.59-4.110.17261420.128827952937
4.11-5.180.14321450.124228112956
5.18-36.260.21221440.172828512995
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)
10.9276-0.30950.07312.8093-0.35111.2934-0.0297-0.0390.0963-0.0041-0.0235-0.51570.06330.09770.01350.159-0.0126-0.00570.22510.02550.2166-31.77839.668-1.225
21.0731-0.4167-0.02072.3816-0.11140.8025-0.0273-0.02270.25240.05160.0012-0.778-0.05460.12230.03140.196-0.0226-0.02320.22340.02110.3711-22.75444.427-0.552
33.47330.15651.47911.91861.18773.49840.07210.1291-0.32210.15420.1-0.82050.30710.4988-0.14070.27360.0337-0.03870.23630.04890.4884-17.06721.6471.687
43.7452-0.0638-1.33441.9784-1.35941.5634-0.03390.14580.3487-0.4829-0.0819-0.22210.2160.93680.06971.00530.0440.35251.3092-0.05860.8727-10.5832.6-25.189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:252 )A25 - 252
2X-RAY DIFFRACTION2( CHAIN A AND RESID 253:469 )A253 - 469
3X-RAY DIFFRACTION3( CHAIN A AND RESID 470:557 )A470 - 557
4X-RAY DIFFRACTION4( CHAIN A AND RESID 558:616 )A558 - 616

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