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- PDB-6wn9: Structure of Staphylococcus aureus peptidoglycan O-acetyltransfer... -

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Basic information

Entry
Database: PDB / ID: 6wn9
TitleStructure of Staphylococcus aureus peptidoglycan O-acetyltransferase A (OatA) C-terminal catalytic domain, Zn-bound
ComponentsAcetyltransferase
KeywordsTRANSFERASE / O-acetyltransferase / peptidoglycan / SGNH hydrolase
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 / plasma membrane
Similarity search - Function
Acyltransferase 3 domain / Acyltransferase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
Acetyltransferase / O-acetyltransferase OatA
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsJones, C.J. / Sychantha, D. / Howell, P.L. / Clarke, A.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT 156353 Canada
Canadian Glycomics Network (GLYCONET) Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for theO-acetyltransferase function of the extracytoplasmic domain of OatA fromStaphylococcus aureus.
Authors: Jones, C.S. / Sychantha, D. / Howell, P.L. / Clarke, A.J.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase
B: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1365
Polymers34,9402
Non-polymers1963
Water7,008389
1
A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5352
Polymers17,4701
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6013
Polymers17,4701
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.510, 78.860, 106.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetyltransferase


Mass: 17469.838 Da / Num. of mol.: 2 / Mutation: E551A, K552A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Gene: E5491_14435 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A4P7P982, UniProt: Q2FV54*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.008 M zinc acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.28167 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28167 Å / Relative weight: 1
ReflectionResolution: 1.55→44.16 Å / Num. obs: 46179 / % possible obs: 93.85 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09615 / Net I/σ(I): 17.53
Reflection shellResolution: 1.55→1.605 Å / Rmerge(I) obs: 0.3412 / Num. unique obs: 2983 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→44.157 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.27
RfactorNum. reflection% reflection
Rfree0.1923 2309 5 %
Rwork0.172 --
obs0.173 46165 93.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.67 Å2 / Biso mean: 24.7862 Å2 / Biso min: 9.57 Å2
Refinement stepCycle: final / Resolution: 1.55→44.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 3 389 2807
Biso mean--18.55 33.73 -
Num. residues----310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.58370.219880.2005164957
1.5837-1.62050.21441050.1981202071
1.6205-1.6610.24841230.1918233980
1.661-1.70590.21121380.1923261892
1.7059-1.75610.23851500.1946285499
1.7561-1.81280.21061530.18172894100
1.8128-1.87760.21751530.17532910100
1.8776-1.95280.19251520.17072894100
1.9528-2.04170.1891520.17362889100
2.0417-2.14930.19491530.16982904100
2.1493-2.2840.19431540.16232918100
2.284-2.46030.19041550.16832946100
2.4603-2.70780.21821540.17932933100
2.7078-3.09960.18921550.17752943100
3.0996-3.90480.18551580.16943003100
3.9048-44.1570.16721660.16153142100
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)
11.99340.00120.24744.83520.45883.3604-0.06040.0135-0.0053-0.0575-0.01560.3280.0309-0.36040.0880.0834-0.0420.00560.19080.01420.154616.8650.2438.262
21.6748-0.3930.6131.8232-0.13582.2733-0.01140.1375-0.0505-0.17320.02160.11450.1151-0.10580.00610.1123-0.0419-0.01250.1318-0.00890.140622.44146.55129.631
30.50570.17870.31551.63570.96884.10790.02960.0618-0.06420.0830.043-0.14650.170.3097-0.07450.06960.0001-0.00810.164-0.02330.147534.10549.20938.336
41.8918-0.17820.20091.37350.03573.3294-0.06120.02050.10080.11070.11750.1121-0.4116-0.0531-0.04240.0723-0.0340.00540.1085-0.00810.133626.72257.46843.246
52.19080.58520.47264.4836-0.14584.12390.0495-0.21170.171-0.0173-0.1798-0.7860.10440.47050.00210.23480.07920.05740.20910.04420.218125.72638.06963.281
62.49860.33661.34813.0297-0.58133.3317-0.02570.1639-0.21-0.39830.1236-0.59880.52670.4998-0.09510.26510.11340.08780.2565-0.01690.316426.15634.25459.671
74.5401-4.79461.27279.2085-1.51972.1923-0.01320.5825-0.6133-0.3377-0.0254-0.51871.42890.63110.0370.66590.05460.09220.3256-0.0770.323419.49725.16653.566
81.28860.4069-0.34342.3246-0.65672.2204-0.05970.1579-0.3235-0.4616-0.1654-0.38730.97850.0836-0.03120.41370.04680.08460.1378-0.00020.231718.87828.40261.743
96.1625-2.30172.49613.5151-1.20136.19370.02840.1554-0.8358-0.56850.13760.11831.3494-0.4241-0.12080.5846-0.12140.02030.2593-0.03080.265110.80524.96458.234
104.2229-0.76570.19223.55870.37212.193-0.09270.1652-0.0655-0.50020.11480.26980.3967-0.3637-0.02850.1777-0.0316-0.0120.1494-0.00010.09612.06236.55661.69
111.8534-0.85951.2998.2716-4.21755.0578-0.00150.2678-0.1314-0.31440.20440.72690.5503-0.7039-0.26690.203-0.0844-0.00220.3828-0.03240.224.23535.20862.257
121.41072.067-0.28836.0653-0.62642.10710.0762-0.1095-0.05840.1785-0.17010.06350.0704-0.25010.04660.08520.02770.00890.16210.00780.118112.16741.30767.99
130.09210.1480.39672.4203-2.4135.7925-0.13620.00050.0387-0.0270.0061-0.0927-0.14170.2340.06710.16160.07180.04280.14240.01590.151619.17351.20856.821
142.81420.4443-2.03214.6819-5.41977.91220.0584-0.3484-0.06950.1596-0.2214-0.1355-0.08810.06890.20120.07540.0316-0.00780.17810.00560.128119.64138.81172.487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 445:489 )A445 - 489
2X-RAY DIFFRACTION2( CHAIN A AND RESID 490:530 )A490 - 530
3X-RAY DIFFRACTION3( CHAIN A AND RESID 531:571 )A531 - 571
4X-RAY DIFFRACTION4( CHAIN A AND RESID 572:599 )A572 - 599
5X-RAY DIFFRACTION5( CHAIN B AND RESID 447:465 )B447 - 465
6X-RAY DIFFRACTION6( CHAIN B AND RESID 466:478 )B466 - 478
7X-RAY DIFFRACTION7( CHAIN B AND RESID 479:489 )B479 - 489
8X-RAY DIFFRACTION8( CHAIN B AND RESID 490:511 )B490 - 511
9X-RAY DIFFRACTION9( CHAIN B AND RESID 512:522 )B512 - 522
10X-RAY DIFFRACTION10( CHAIN B AND RESID 523:538 )B523 - 538
11X-RAY DIFFRACTION11( CHAIN B AND RESID 539:552 )B539 - 552
12X-RAY DIFFRACTION12( CHAIN B AND RESID 553:571 )B553 - 571
13X-RAY DIFFRACTION13( CHAIN B AND RESID 572:580 )B572 - 580
14X-RAY DIFFRACTION14( CHAIN B AND RESID 581:601 )B581 - 601

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