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- PDB-5v0z: Crystal structure of Galactoside O-acetyltransferase complex with... -

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Basic information

Entry
Database: PDB / ID: 5v0z
TitleCrystal structure of Galactoside O-acetyltransferase complex with CoA (P32 space group).
ComponentsPutative acetyltransferase SACOL2570
KeywordsTRANSFERASE / Structural Genomics / CSGID / acetyltransferase / Coenzyme-A / 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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsCzub, M.P. / Porebski, P.J. / Knapik, A.A. / Niedzialkowska, E. / 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 Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal structure of Galactoside O-acetyltransferase complex with CoA (P32 space group).
Authors: Czub, M.P. / Porebski, P.J. / Knapik, A.A. / Niedzialkowska, E. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Putative acetyltransferase SACOL2570
B: Putative acetyltransferase SACOL2570
C: Putative acetyltransferase SACOL2570
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,26750
Polymers67,2513
Non-polymers3,01647
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-25 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.434, 75.434, 93.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Putative acetyltransferase SACOL2570


Mass: 22417.127 Da / Num. of mol.: 3
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) RIL
References: UniProt: Q5HCZ5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 6 types, 871 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 31 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1uL of 15 mg/ml protein incubated with 5mM CoA 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 ...Details: 1uL of 15 mg/ml protein incubated with 5mM CoA 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).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / 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: 1.26→50 Å / Num. obs: 159888 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.027 / Rrim(I) all: 0.048 / Χ2: 0.606 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.26-1.282.80.3452.10.9250.250.4280.44899.8
1.28-1.312.90.3160.9340.2240.3890.43399.7
1.31-1.332.90.2890.9510.2060.3560.43599.6
1.33-1.362.80.2450.9690.1740.3020.43499.4
1.36-1.392.80.2240.9670.1610.2770.4599.6
1.39-1.422.60.1910.9760.1410.2390.44698.6
1.42-1.452.90.1650.9810.1160.2030.45599.8
1.45-1.492.90.1310.9870.0920.1610.46799.7
1.49-1.542.90.1080.990.0760.1330.4899.8
1.54-1.592.90.0920.9930.0650.1130.47299.7
1.59-1.642.80.0790.9950.0570.0970.47599.2
1.64-1.712.90.0680.9960.0480.0840.48198.9
1.71-1.7930.0580.9970.0410.0710.49999.9
1.79-1.8830.0490.9980.0340.060.53899.7
1.88-22.90.0420.9980.0290.0520.61799.7
2-2.152.90.0380.9980.0260.0460.70598.3
2.15-2.373.10.0340.9980.0230.0410.71899.9
2.37-2.7130.0340.9980.0230.0410.81799.7
2.71-3.4230.0310.9990.0210.0381.07197.9
3.42-5030.0340.9980.0220.041.52798.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U2K

5u2k


Resolution: 1.26→50 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.505 / SU ML: 0.028 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.041
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1642 8155 5.1 %RANDOM
Rwork0.1361 ---
obs0.1375 151162 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.91 Å2 / Biso mean: 19.58 Å2 / Biso min: 6.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å2-0 Å2
2---0.16 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4428 0 355 826 5609
Biso mean--33.51 40.11 -
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195047
X-RAY DIFFRACTIONr_bond_other_d0.0020.024403
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9336924
X-RAY DIFFRACTIONr_angle_other_deg1.204310294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08624.915234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09815764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2671519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025896
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021015
X-RAY DIFFRACTIONr_rigid_bond_restr4.27134995
X-RAY DIFFRACTIONr_sphericity_free35.3725462
X-RAY DIFFRACTIONr_sphericity_bonded16.46155166
LS refinement shellResolution: 1.26→1.293 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 549 -
Rwork0.249 11274 -
all-11823 -
obs--99.78 %

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