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- PDB-6n1x: BshA from Staphylococcus aureus complexed with UDP and N-acetylgl... -

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Basic information

Entry
Database: PDB / ID: 6n1x
TitleBshA from Staphylococcus aureus complexed with UDP and N-acetylglucosamine
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Bacillithiol / Glycosyltransferase / UDP-N-acetylglucosamine / GT-B
Function / homology
Function and homology information


bacillithiol biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity
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
2-acetamido-2-deoxy-alpha-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus CN1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1613
Polymers42,5361
Non-polymers6252
Water1,31573
1
A: Glycosyltransferase
hetero molecules

A: Glycosyltransferase
hetero molecules

A: Glycosyltransferase
hetero molecules

A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,64512
Polymers170,1444
Non-polymers2,5018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area20850 Å2
ΔGint-105 kcal/mol
Surface area47020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.143, 135.143, 135.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Glycosyltransferase


Mass: 42535.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus CN1 (bacteria)
Gene: SAKOR_01400 / Production host: Escherichia coli (E. coli)
References: UniProt: T1Y9F7, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 4.84 Å3/Da / Density % sol: 74.56 % / Description: medium cubes
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M sodium formate, 6% polyethylene glycol 3350, 2.5 mM UDP-N-acetylglucosamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 34569 / % possible obs: 100 % / Redundancy: 22.4 % / Biso Wilson estimate: 39.27 Å2 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.042 / Rrim(I) all: 0.197 / Χ2: 1.222 / Net I/σ(I): 5.1 / Num. measured all: 773023
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.3921.91.97917130.7050.4322.0261.013100
2.39-2.4322.41.79816880.740.3881.841.01100
2.43-2.4822.51.56917150.7970.3381.6051.042100
2.48-2.5322.61.30616950.8570.281.3351.052100
2.53-2.5922.71.15717170.8740.2481.1841.06100
2.59-2.6522.80.99417060.9030.2131.0171.083100
2.65-2.7122.70.82317210.940.1760.8421.094100
2.71-2.7922.80.71917180.9470.1540.7361.109100
2.79-2.8722.70.617230.960.1280.6141.131100
2.87-2.9622.80.45517150.9770.0970.4651.177100
2.96-3.0722.80.37417330.9850.080.3821.199100
3.07-3.1922.60.31717120.9890.0680.3241.211100
3.19-3.3322.80.23517190.9940.050.2411.271100
3.33-3.5122.70.17817110.9970.0380.1831.307100
3.51-3.7322.70.13217410.9980.0280.1351.373100
3.73-4.0222.50.09717190.9990.0210.0991.429100
4.02-4.4222.40.07417640.9990.0160.0761.485100
4.42-5.0622.10.05717480.9990.0120.0591.464100
5.06-6.3621.90.06517680.9990.0140.0661.453100
6.36-3019.10.045184310.0110.0461.49199.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D9T

6d9t


Resolution: 2.35→27.029 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.1
RfactorNum. reflection% reflection
Rfree0.1963 1882 5.45 %
Rwork0.1733 --
obs0.1746 34554 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.39 Å2 / Biso mean: 42.0749 Å2 / Biso min: 23.37 Å2
Refinement stepCycle: final / Resolution: 2.35→27.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 40 73 3048
Biso mean--35.11 40.13 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083031
X-RAY DIFFRACTIONf_angle_d0.9134109
X-RAY DIFFRACTIONf_chiral_restr0.052481
X-RAY DIFFRACTIONf_plane_restr0.006519
X-RAY DIFFRACTIONf_dihedral_angle_d5.6241817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.349-2.41250.28061530.25625012654
2.4125-2.48340.27581410.228324672608
2.4834-2.56350.24331250.215125052630
2.5635-2.6550.24851380.215125132651
2.655-2.76120.23431390.195924692608
2.7612-2.88680.22771110.198925442655
2.8868-3.03880.22021590.193424702629
3.0388-3.22890.24691500.198525002650
3.2289-3.47770.21271670.192424882655
3.4777-3.82680.19831420.157625262668
3.8268-4.37850.13751460.144525252671
4.3785-5.50880.15811280.135425642692
5.5088-27.03040.17731830.159126002783

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