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- PDB-5ug1: Structure of Streptococcus pneumoniae peptidoglycan O-acetyltrans... -

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Basic information

Entry
Database: PDB / ID: 5ug1
TitleStructure of Streptococcus pneumoniae peptidoglycan O-acetyltransferase A (OatA) C-terminal catalytic domain with methylsulfonyl adduct
ComponentsAcyltransferase
KeywordsTRANSFERASE / atypical alpha/beta hydrolase fold / catalytic triad / covalent complex
Function / homology
Function and homology information


: / lipopolysaccharide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / membrane => GO:0016020 / membrane
Similarity search - Function
Acyltransferase 3 domain / Acyltransferase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
methanesulfonic acid / Acyltransferase / Acyltransferase 3 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsSychantha, D. / Jones, C. / Little, D.J. / Moynihan, P.J. / Robinson, H. / Galley, N.F. / Roper, D.I. / Dowson, C.G. / Howell, P.L. / Clarke, A.J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Glycomics Network Canada
Canadian Institute for Health ResearchTGC 114045 Canada
Canadian Institute for Health ResearchMOP 43998 Canada
CitationJournal: PLoS Pathog. / Year: 2017
Title: In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA).
Authors: Sychantha, D. / Jones, C.S. / Little, D.J. / Moynihan, P.J. / Robinson, H. / Galley, N.F. / Roper, D.I. / Dowson, C.G. / Howell, P.L. / Clarke, A.J.
History
DepositionJan 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5543
Polymers19,4351
Non-polymers1192
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.481, 70.481, 136.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Acyltransferase


Mass: 19434.877 Da / Num. of mol.: 1 / Mutation: UNP residues 427-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: oatA_2, oatA, ERS020148_01611, ERS021300_00524, ERS022045_04974
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0T8LL95, UniProt: Q8CY83*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-03S / methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O3S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES:NaOH, 1.2 M Sodium Citrate Tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25.89 Å / Num. obs: 10191 / % possible obs: 98 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11.39 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 4 / Num. unique obs: 1005 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHASERmodel building
Cootmodel building
RefinementResolution: 2.1→25.888 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.12
RfactorNum. reflection% reflection
Rfree0.2347 1018 10 %
Rwork0.1722 --
obs0.1786 10180 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→25.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 5 156 1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071390
X-RAY DIFFRACTIONf_angle_d0.7681894
X-RAY DIFFRACTIONf_dihedral_angle_d12.343840
X-RAY DIFFRACTIONf_chiral_restr0.047223
X-RAY DIFFRACTIONf_plane_restr0.005244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21070.31551380.2121247X-RAY DIFFRACTION95
2.2107-2.34910.29141410.19461267X-RAY DIFFRACTION97
2.3491-2.53040.24081410.20291271X-RAY DIFFRACTION98
2.5304-2.78470.33521450.21551298X-RAY DIFFRACTION98
2.7847-3.18710.23681450.19111314X-RAY DIFFRACTION99
3.1871-4.0130.22061490.1421341X-RAY DIFFRACTION99
4.013-25.89030.17451590.15021424X-RAY DIFFRACTION99
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)
16.0391-0.63813.79671.70970.86158.05710.06280.37380.1833-0.0828-0.0769-0.1897-0.05890.39730.03470.1734-0.01170.06140.20150.02050.2395-7.962424.4465-23.8922
21.4431-0.67180.12372.9961-0.21814.30360.0135-0.04260.0878-0.0595-0.0135-0.1002-0.2027-0.0727-0.0060.18120.0166-0.00910.1764-0.01560.2402-18.644131.4209-20.4813
35.69480.5874.61891.27790.74913.8185-0.0522-0.293-0.14190.1610.1771-0.0553-0.0928-0.2752-0.15760.21670.01110.00520.25740.01290.2234-17.62424.3316-7.4677
47.2449-4.5029-1.60853.15771.90992.6639-0.2321-0.5812-0.6910.40430.46260.42151.0861-0.1895-0.21550.3202-0.0266-0.01950.2460.0440.2602-8.102315.0044-6.8902
54.10940.433.47693.3878-2.05164.7163-0.2135-0.27820.3280.01360.1271-0.289-0.14240.23030.12710.2280.0283-0.02040.3009-0.01570.30190.870121.0741-6.8838
66.4258-2.39916.25742.3993-1.6196.44840.65670.3156-0.4524-0.1932-0.2010.0020.76380.0702-0.52250.2717-0.00370.04530.2077-0.02470.2407-13.18116.0087-20.2145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 427 through 463 )
2X-RAY DIFFRACTION2chain 'A' and (resid 464 through 516 )
3X-RAY DIFFRACTION3chain 'A' and (resid 517 through 552 )
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 563 )
5X-RAY DIFFRACTION5chain 'A' and (resid 564 through 575 )
6X-RAY DIFFRACTION6chain 'A' and (resid 576 through 605 )

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