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- PDB-6d9t: BshA from Staphylococcus aureus complexed with UDP -

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Basic information

Entry
Database: PDB / ID: 6d9t
TitleBshA from Staphylococcus aureus complexed with UDP
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / Bacillithiol / Glycosyltransferase / UDP-N-acetylglucosamine / GT-B / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


phosphatidylinositol alpha-mannosyltransferase / phosphatidyl-myo-inositol alpha-mannosyltransferase / phosphatidylinositol alpha-mannosyltransferase activity / bacillithiol biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
Similarity search - Function
N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glycosyl transferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRoyer, C.R. / Cook, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM117488 United States
CitationJournal: Protein Sci. / Year: 2019
Title: A structural and functional analysis of the glycosyltransferase BshA from Staphylococcus aureus: Insights into the reaction mechanism and regulation of bacillithiol production.
Authors: Royer, C.J. / Cook, P.D.
History
DepositionApr 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: 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

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Assembly

Deposited unit
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0133
Polymers45,2051
Non-polymers8082
Water4,666259
1
A: Glycosyl transferase
hetero molecules

A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0266
Polymers90,4092
Non-polymers1,6174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6430 Å2
ΔGint-62 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.380, 135.380, 135.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

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Components

#1: Protein Glycosyl transferase / N-acetyl-alpha-D-glucosaminyl L-malate synthase / N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA


Mass: 45204.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: pimB_2, BTN44_05260, EP54_02400, EQ90_10145, ERS365775_02315
Production host: Escherichia coli (E. coli)
References: UniProt: A0A068A5A2, phosphatidylinositol alpha-mannosyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 4.57 Å3/Da / Density % sol: 73.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% (v/v) Jeffamine ED-2001 0.05 M imidazole 10 mM HEPES 25 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→55.27 Å / Num. obs: 55977 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 21.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.062 / Rrim(I) all: 0.14 / Net I/σ(I): 8.7 / Num. measured all: 280701 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.0550.65141330.7550.3240.729100
8.95-55.274.40.056980.9960.0260.05699.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D01

5d01


Resolution: 2→55.269 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.71
RfactorNum. reflection% reflection
Rfree0.1884 2766 4.95 %
Rwork0.1682 --
obs0.1692 55918 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.99 Å2 / Biso mean: 25.3255 Å2 / Biso min: 9.3 Å2
Refinement stepCycle: final / Resolution: 2→55.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 50 259 3266
Biso mean--26.49 33.72 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083079
X-RAY DIFFRACTIONf_angle_d0.8724177
X-RAY DIFFRACTIONf_chiral_restr0.057481
X-RAY DIFFRACTIONf_plane_restr0.006526
X-RAY DIFFRACTIONf_dihedral_angle_d5.5432555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0004-2.03490.25951520.234826132765
2.0349-2.07190.23811570.218325842741
2.0719-2.11180.22921320.204726542786
2.1118-2.15490.22241240.197326542778
2.1549-2.20170.22311240.197726392763
2.2017-2.2530.2131410.188426462787
2.253-2.30930.21691260.181426362762
2.3093-2.37170.20991530.179526062759
2.3717-2.44150.18641120.176126892801
2.4415-2.52030.19141380.172926522790
2.5203-2.61040.22391120.178326962808
2.6104-2.71490.21971350.171525882723
2.7149-2.83850.2031510.17426522803
2.8385-2.98810.17791440.167826652809
2.9881-3.17530.20521500.178926342784
3.1753-3.42050.20041390.174526662805
3.4205-3.76460.16131170.158327062823
3.7646-4.30920.18131570.141826542811
4.3092-5.42840.13361570.126527132870
5.4284-55.28970.15281450.15928052950

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