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- PDB-5egl: The structural and biochemical characterization of acyl-coa hydro... -

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Basic information

Entry
Database: PDB / ID: 5egl
TitleThe structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus in complex with Butyryl Coenzyme A, Coenzyme A, and Coenzyme A disulfide
ComponentsAcyl CoA Hydrolase
KeywordsHYDROLASE / Acyl CoA thioesterase / Staphylococcus aureus / Coenzyme A / Hotdog thioesterase
Function / homology
Function and homology information


thiolester hydrolase activity
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-5NG / Butyryl Coenzyme A / COENZYME A / HotDog ACOT-type domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhandokar, Y.B. / Srivastava, P.S. / Forwood, J.K.
CitationJournal: To Be Published
Title: The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus
Authors: Khandokar, Y.B. / Srivastava, P.S. / Forwood, J.K.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl CoA Hydrolase
B: Acyl CoA Hydrolase
C: Acyl CoA Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1166
Polymers59,9783
Non-polymers3,1383
Water3,963220
1
A: Acyl CoA Hydrolase
B: Acyl CoA Hydrolase
C: Acyl CoA Hydrolase
hetero molecules

A: Acyl CoA Hydrolase
B: Acyl CoA Hydrolase
C: Acyl CoA Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,23212
Polymers119,9566
Non-polymers6,2766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area20450 Å2
ΔGint-120 kcal/mol
Surface area40170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.260, 142.260, 163.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-380-

HOH

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Components

#1: Protein Acyl CoA Hydrolase


Mass: 19992.623 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV1878 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS / References: UniProt: A0A0H3K033
#2: Chemical ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O17P3S
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-5NG / [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate / CoA-disulfide


Mass: 1533.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H70N14O32P6S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 4M Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2014
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→39.84 Å / Num. obs: 57467 / % possible obs: 99.99 % / Redundancy: 2 % / Rmerge(I) obs: 0.02717 / Net I/σ(I): 13.83
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.23 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1894refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCP

4ncp


Resolution: 2.1→39.835 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 2939 5.11 %
Rwork0.2125 --
obs0.2142 57459 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 197 220 4312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064181
X-RAY DIFFRACTIONf_angle_d1.1125682
X-RAY DIFFRACTIONf_dihedral_angle_d15.1811524
X-RAY DIFFRACTIONf_chiral_restr0.041619
X-RAY DIFFRACTIONf_plane_restr0.005706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13440.29511110.27542573X-RAY DIFFRACTION100
2.1344-2.17120.34991420.27332547X-RAY DIFFRACTION100
2.1712-2.21070.27811380.25822554X-RAY DIFFRACTION100
2.2107-2.25320.25771260.24942573X-RAY DIFFRACTION100
2.2532-2.29920.28491570.24662539X-RAY DIFFRACTION100
2.2992-2.34920.30151510.24352536X-RAY DIFFRACTION100
2.3492-2.40390.27941500.24092542X-RAY DIFFRACTION100
2.4039-2.4640.291460.23792559X-RAY DIFFRACTION100
2.464-2.53060.29271340.24392564X-RAY DIFFRACTION100
2.5306-2.6050.28971370.24522564X-RAY DIFFRACTION100
2.605-2.68910.27521390.23942583X-RAY DIFFRACTION100
2.6891-2.78520.26371200.24462610X-RAY DIFFRACTION100
2.7852-2.89670.26291530.24442571X-RAY DIFFRACTION100
2.8967-3.02850.27921370.24692581X-RAY DIFFRACTION100
3.0285-3.18810.27781370.23532595X-RAY DIFFRACTION100
3.1881-3.38770.26051510.22062601X-RAY DIFFRACTION100
3.3877-3.64910.23331330.20682617X-RAY DIFFRACTION100
3.6491-4.0160.23321340.18632631X-RAY DIFFRACTION100
4.016-4.59640.18631440.16022646X-RAY DIFFRACTION100
4.5964-5.78810.1841370.17222704X-RAY DIFFRACTION100
5.7881-39.84250.24351620.20742830X-RAY DIFFRACTION100

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