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

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Basic information

Entry
Database: PDB / ID: 6vjp
TitleStructure of Staphylococcus aureus peptidoglycan O-acetyltransferase A (OatA) C-terminal catalytic domain
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 / MOLECULAR REPLACEMENT / Resolution: 1.711 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 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
DepositionJan 16, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)34,9864
Polymers34,9402
Non-polymers462
Water4,828268
1
A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4932
Polymers17,4701
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4932
Polymers17,4701
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.347, 61.303, 67.690
Angle α, β, γ (deg.)90.000, 100.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acetyltransferase


Mass: 17469.771 Da / Num. of mol.: 2 / Mutation: K495A, K496A
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 27% PEG 6000, 0.015 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.99961 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99961 Å / Relative weight: 1
ReflectionResolution: 1.711→28.78 Å / Num. obs: 36587 / % possible obs: 99.36 % / Redundancy: 1.96 % / CC1/2: 0.999 / Net I/σ(I): 17.32
Reflection shellResolution: 1.711→1.773 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 3545 / CC1/2: 0.633 / % possible all: 96.12

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OatA Zn

Resolution: 1.711→28.778 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21
RfactorNum. reflection% reflection
Rfree0.195 2000 5.47 %
Rwork0.166 --
obs0.1676 36580 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.11 Å2 / Biso mean: 31.8733 Å2 / Biso min: 16.43 Å2
Refinement stepCycle: final / Resolution: 1.711→28.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 2 268 2667
Biso mean--26.85 41.88 -
Num. residues----308
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.711-1.75360.40391340.3757232693
1.7536-1.8010.26641420.25752451100
1.801-1.8540.23961430.20322468100
1.854-1.91390.23511440.19852485100
1.9139-1.98230.23481420.18122449100
1.9823-2.06160.22391420.17392468100
2.0616-2.15540.19511430.16492461100
2.1554-2.2690.22431450.16272499100
2.269-2.41110.19191420.17212473100
2.4111-2.59710.19321440.16822478100
2.5971-2.85830.18171440.16982492100
2.8583-3.27140.20371450.1672502100
3.2714-4.11970.18231430.14222486100
4.1197-28.7780.15831470.15132542100
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)
16.48742.84941.02358.93635.46753.9996-0.02670.4833-0.1168-0.24040.1061-0.0576-0.08990.1313-0.08310.20750.0168-0.01440.23720.030.1873-20.1981.6338-12.9246
25.31920.22954.40011.7865-0.06254.984-0.1592-0.23330.05470.13590.0985-0.1194-0.2566-0.25860.06680.17130.0180.01670.18780.00830.2078-24.8972.0988-0.2277
36.2851.14191.04862.1849-0.63612.7128-0.012-0.0754-0.02470.01040.02370.0058-0.03840.026-0.02160.1653-0.014-0.0130.19370.040.1972-16.2055-5.75962.1891
48.38993.1604-0.41073.2724-1.86123.06920.0122-0.0335-0.3642-0.1777-0.029-0.03550.1941-0.0086-0.00160.17110.022-0.00030.1944-0.02730.2386-9.7995-6.319-11.1058
56.173.50242.75818.25753.20636.20960.0913-0.4898-0.1248-0.3372-0.34460.03220.2638-0.67350.18820.3141-0.0120.0340.2647-0.01070.22113.39827.0296-29.0573
65.21464.7875-3.78426.9867-4.32065.8922-0.06720.0054-0.1461-0.32690.0204-0.26860.1550.21220.05740.20040.03020.03410.1571-0.02840.21848.64826.6867-24.921
75.24882.7791.73355.56435.41695.5919-0.14710.2028-0.1559-1.41130.3099-0.74710.00580.0807-0.13860.6149-0.01640.13320.24990.02660.37.624612.9539-39.7503
82.05530.10861.80525.25211.6174.10430.36090.282-0.6025-0.8825-0.17740.00150.0928-0.237-0.23610.4799-0.0241-0.03850.2642-0.03510.2873-2.21325.2365-37.8457
95.2642.12211.42675.23160.54122.2686-0.11010.17320.3002-0.7101-0.00580.1051-0.3802-0.1510.11140.41380.02940.03550.2173-0.01230.18563.016618.9959-33.6012
104.13922.31071.91785.13732.07626.78120.03230.07590.0139-0.475-0.07190.43440.1927-0.50750.14310.32230.0183-0.06610.2587-0.00030.2749-5.102613.0301-31.3346
116.33032.31320.64774.4284-0.28055.6468-0.0936-0.01230.0704-0.213-0.0439-0.0989-0.55390.17340.1040.27820.0040.01520.1979-0.01580.25179.562125.6167-21.2549
126.11593.97013.20614.3151.71563.5155-0.1678-0.29340.5693-0.442-0.03660.4507-0.5214-0.4560.29660.36420.0895-0.0280.24590.00570.2897-1.269626.5662-27.2391
138.0488-0.56456.99171.8515-0.60138.89360.058-0.23430.0117-0.0685-0.04050.2849-0.1571-0.46050.03910.17790.03570.00660.2034-0.02790.2313-0.331118.5193-18.7648
143.73763.34652.88423.63913.51566.4604-0.14880.2951-0.2407-0.30450.416-0.55990.12010.5551-0.32340.19390.00260.0150.2256-0.01570.257115.253416.8117-15.4206
158.137-1.82846.91176.8241-1.12958.1877-0.0466-0.3975-0.316-0.11970.06930.37120.0073-0.5218-0.02960.16770.00070.0460.2223-0.00450.2203-0.28458.9363-17.3157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 445 through 478 )A445 - 478
2X-RAY DIFFRACTION2chain 'A' and (resid 479 through 522 )A479 - 522
3X-RAY DIFFRACTION3chain 'A' and (resid 523 through 560 )A523 - 560
4X-RAY DIFFRACTION4chain 'A' and (resid 561 through 599 )A561 - 599
5X-RAY DIFFRACTION5chain 'B' and (resid 445 through 452 )B445 - 452
6X-RAY DIFFRACTION6chain 'B' and (resid 453 through 478 )B453 - 478
7X-RAY DIFFRACTION7chain 'B' and (resid 479 through 489 )B479 - 489
8X-RAY DIFFRACTION8chain 'B' and (resid 490 through 498 )B490 - 498
9X-RAY DIFFRACTION9chain 'B' and (resid 499 through 522 )B499 - 522
10X-RAY DIFFRACTION10chain 'B' and (resid 523 through 530 )B523 - 530
11X-RAY DIFFRACTION11chain 'B' and (resid 531 through 538 )B531 - 538
12X-RAY DIFFRACTION12chain 'B' and (resid 539 through 552 )B539 - 552
13X-RAY DIFFRACTION13chain 'B' and (resid 553 through 571 )B553 - 571
14X-RAY DIFFRACTION14chain 'B' and (resid 572 through 580 )B572 - 580
15X-RAY DIFFRACTION15chain 'B' and (resid 581 through 597 )B581 - 597

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