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- PDB-5u2k: Crystal structure of Galactoside O-acetyltransferase complex with... -

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Basic information

Entry
Database: PDB / ID: 5u2k
TitleCrystal structure of Galactoside O-acetyltransferase complex with CoA (H3 space group)
ComponentsGalactoside O-acetyltransferase
KeywordsTRANSFERASE / CSGID / Galactoside O-acetyltransferase / CoA / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


galactoside O-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily ...Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
COENZYME A / PHOSPHATE ION / Putative acetyltransferase SACOL2570
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.38 Å
AuthorsCzub, M.P. / Porebski, P.J. / Knapik, A.A. / Niedzialkowska, E. / Siuda, M.K. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of Galactoside O-acetyltransferase complex with CoA (H3 space group)
Authors: Czub, M.P. / Porebski, P.J. / Knapik, A.A. / Niedzialkowska, E. / Siuda, M.K. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactoside O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3539
Polymers22,1451
Non-polymers1,2088
Water4,558253
1
A: Galactoside O-acetyltransferase
hetero molecules

A: Galactoside O-acetyltransferase
hetero molecules

A: Galactoside O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,06027
Polymers66,4353
Non-polymers3,62524
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 area14490 Å2
ΔGint-41 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.424, 75.424, 93.482
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

21A-546-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Galactoside O-acetyltransferase


Mass: 22144.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: SACOL2570 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus RIL
References: UniProt: Q5HCZ5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 261 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1uL of 15 mg/ml protein were mixed with 1 uL of 25% w/v PEG 3350, 250 mM Sodium/Potassium phosphate, 30% v/v Ethylene glycol and equilibrated against well solution in 15 Well Crystallization ...Details: 1uL of 15 mg/ml protein were mixed with 1 uL of 25% w/v PEG 3350, 250 mM Sodium/Potassium phosphate, 30% v/v Ethylene glycol and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked in CoA to final concentration of 5 mM.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2016
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 40705 / % possible obs: 99.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.032 / Rrim(I) all: 0.073 / Χ2: 0.787 / Net I/σ(I): 5.8 / Num. measured all: 204029
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.38-1.44.70.4870.8481100
1.4-1.434.50.4390.857199.4
1.43-1.464.90.3670.909199.4
1.46-1.495.10.2920.9461100
1.49-1.525.10.2420.9621100
1.52-1.555.10.2160.9631100
1.55-1.5950.1920.9711100
1.59-1.6450.1590.98199.9
1.64-1.684.60.1480.978198.9
1.68-1.745.10.1280.9871100
1.74-1.85.30.110.9911100
1.8-1.875.20.0950.9941100
1.87-1.965.20.0820.9951100
1.96-2.0650.0720.995199.9
2.06-2.194.90.0630.994198.6
2.19-2.365.40.0610.9961100
2.36-2.65.30.0590.9961100
2.6-2.974.90.060.994199.9
2.97-3.7550.0570.996199.8
3.75-504.90.0550.997199.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
SCALEPACKdata scaling
RefinementResolution: 1.38→50 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.708 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0508 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.053
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 1870 4.6 %RANDOM
Rwork0.1256 ---
obs0.1275 38831 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 21.028 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å2-0 Å2
2---0.23 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 106 254 1835
Biso mean--30.96 38.06 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191731
X-RAY DIFFRACTIONr_bond_other_d0.0020.021587
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9152379
X-RAY DIFFRACTIONr_angle_other_deg1.972.9393671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44623.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39115263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.146157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02407
X-RAY DIFFRACTIONr_rigid_bond_restr11.79131627
X-RAY DIFFRACTIONr_sphericity_bonded12.39111572
LS refinement shellResolution: 1.38→1.416 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 140 -
Rwork0.226 2866 -
all-3006 -
obs--99.87 %

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