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

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Basic information

Entry
Database: PDB / ID: 5ufy
TitleStructure of Streptococcus pneumoniae peptidoglycan O-acetyltransferase A (OatA) C-terminal catalytic domain
ComponentsAcyltransferase
KeywordsTRANSFERASE / atytpical alpha/beta hydrolase / catalytic triad
Function / homology
Function and homology information


lipopolysaccharide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / membrane => GO:0016020 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / membrane / plasma membrane
Similarity search - Function
: / Acyltransferase 3 domain / Acyltransferase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
Acyltransferase / Acyltransferase 3 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4402
Polymers24,4171
Non-polymers231
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.203, 70.203, 135.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-957-

HOH

21A-979-

HOH

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Components

#1: Protein Acyltransferase


Mass: 24417.191 Da / Num. of mol.: 1 / Mutation: UNP residues 421-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: oatA_2, oatA, oatA_1, oatA_3, ERS020138_01729, ERS020158_01919, ERS020525_00845, ERS020528_00979, ERS020532_00615, ERS020726_01157, ERS020726_01160, ERS020726_01165, ERS021733_04500, ERS232524_00457
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: A0A0T7JIN8, UniProt: Q8CY83*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 1.71 Å3/Da / Density % sol: 28.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.8 M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 65286 / % possible obs: 99.1 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 64.2
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 13.2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→40.051 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.46
RfactorNum. reflection% reflection
Rfree0.1681 1991 3.09 %
Rwork0.1502 --
obs0.1508 64409 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.12→40.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 1 243 1610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061411
X-RAY DIFFRACTIONf_angle_d0.9391916
X-RAY DIFFRACTIONf_dihedral_angle_d14.489517
X-RAY DIFFRACTIONf_chiral_restr0.075225
X-RAY DIFFRACTIONf_plane_restr0.007247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1197-1.14770.20181370.20814281X-RAY DIFFRACTION96
1.1477-1.17870.19741390.17534306X-RAY DIFFRACTION97
1.1787-1.21340.18651390.17034370X-RAY DIFFRACTION97
1.2134-1.25250.191370.1664352X-RAY DIFFRACTION98
1.2525-1.29730.16531390.16954374X-RAY DIFFRACTION98
1.2973-1.34930.17681400.16414404X-RAY DIFFRACTION98
1.3493-1.41070.18991420.16054419X-RAY DIFFRACTION99
1.4107-1.4850.15911410.15474446X-RAY DIFFRACTION99
1.485-1.57810.181440.14464464X-RAY DIFFRACTION99
1.5781-1.69990.14771430.14634505X-RAY DIFFRACTION100
1.6999-1.8710.16231440.15244522X-RAY DIFFRACTION100
1.871-2.14170.15251450.13964557X-RAY DIFFRACTION100
2.1417-2.69830.1681470.14224607X-RAY DIFFRACTION100
2.6983-40.07630.16891540.14644811X-RAY DIFFRACTION100
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)
11.5798-0.87020.4641.41110.10151.7383-0.01440.07140.0489-0.0175-0.0045-0.1272-0.01680.13550.00830.0613-0.01320.01920.0897-0.00430.0875-10.277527.6017-23.7559
23.85581.01850.42043.2950.2424.9729-0.01320.11890.0355-0.19160.0878-0.0345-0.0247-0.218-0.08370.03660.01970.02190.0405-0.020.0555-16.675227.9441-28.8976
32.5011-0.21732.22983.02851.6616.351-0.1681-0.18050.13540.10450.0468-0.0803-0.1871-0.12840.14010.0754-0.00270.00320.0687-0.00230.0814-18.983732.9951-11.8007
41.99930.50822.43664.2980.65758.35020.0060.00960.0106-0.0344-0.00410.0714-0.058-0.0982-0.02170.0358-0.00970.01950.094-0.00690.0706-22.947725.7656-24.3925
53.17-1.2931.46042.40662.27516.6708-0.0331-0.24370.05870.17480.2619-0.2497-0.00470.1853-0.21750.0805-0.0161-0.01190.08890.00040.0969-9.031425.7557-2.0689
61.93860.12311.18250.57410.04761.92420.0962-0.0887-0.12450.0862-0.004-0.07360.1311-0.0029-0.07620.0902-0.0094-0.02330.08070.00850.0889-12.858420.6775-8.4661
74.6459-1.37663.93531.6702-0.84043.54060.24040.3236-0.32760.0389-0.0173-0.03460.27930.2169-0.26170.11040.01080.0070.1056-0.01420.1-13.398616.0441-20.2103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 427 through 476 )
2X-RAY DIFFRACTION2chain 'A' and (resid 477 through 487 )
3X-RAY DIFFRACTION3chain 'A' and (resid 488 through 506 )
4X-RAY DIFFRACTION4chain 'A' and (resid 507 through 515 )
5X-RAY DIFFRACTION5chain 'A' and (resid 516 through 527 )
6X-RAY DIFFRACTION6chain 'A' and (resid 528 through 575 )
7X-RAY DIFFRACTION7chain 'A' and (resid 576 through 605 )

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