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- PDB-5d01: Crystal structure of BshA from B. subtilis complexed with N-acety... -

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Basic information

Entry
Database: PDB / ID: 5d01
TitleCrystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate
ComponentsN-acetyl-alpha-D-glucosaminyl L-malate synthase
KeywordsTRANSFERASE / Bacillithiol / glycosyltransferase / GlcNAc / Gram-positive
Function / homology
Function and homology information


bacillithiol biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / 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
Chem-GMT / N-acetyl-alpha-D-glucosaminyl L-malate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsCook, P.D. / Winchell, K.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM093507 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM030910 United States
CitationJournal: Biochemistry / Year: 2016
Title: A Structural, Functional, and Computational Analysis of BshA, the First Enzyme in the Bacillithiol Biosynthesis Pathway.
Authors: Winchell, K.R. / Egeler, P.W. / VanDuinen, A.J. / Jackson, L.B. / Karpen, M.E. / Cook, P.D.
History
DepositionAug 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2May 1, 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
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: N-acetyl-alpha-D-glucosaminyl L-malate synthase
B: N-acetyl-alpha-D-glucosaminyl L-malate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1344
Polymers84,4592
Non-polymers6752
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-32 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.060, 163.250, 97.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein N-acetyl-alpha-D-glucosaminyl L-malate synthase / GlcNAc-Mal synthase / L-malic acid glycosyltransferase BshA


Mass: 42229.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: bshA, jojH, ypjH, BSU22460 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P42982, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Sugar ChemComp-GMT / (2S)-2-{[2-acetamido-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid / (2S)-2-{[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid / (2S)-2-{[2-acetamido-2-deoxy-alpha-D-glucosyl]oxy}butanedioic acid / (2S)-2-{[2-acetamido-2-deoxy-D-glucosyl]oxy}butanedioic acid / (2S)-2-{[2-acetamido-2-deoxy-glucosyl]oxy}butanedioic acid


Type: D-saccharide / Mass: 337.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO10
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM ammonium citrate, 10% (w/v) PEG 3400, 10 mM HEPES, 25 mM NaCl, 5 mM UDP-N-acetylglucosamine, 5 mM malate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.02→97.25 Å / Num. obs: 46645 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.5
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MBO

3mbo


Resolution: 2.02→81.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.581 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 2313 5 %RANDOM
Rwork0.1929 ---
obs0.1959 44313 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.15 Å2 / Biso mean: 44.6 Å2 / Biso min: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å20 Å2
2--0.51 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 2.02→81.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 46 181 5733
Biso mean--32.67 42.1 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195686
X-RAY DIFFRACTIONr_bond_other_d0.0010.025585
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9837697
X-RAY DIFFRACTIONr_angle_other_deg0.834312875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91624.934229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.362151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4121522
X-RAY DIFFRACTIONr_chiral_restr0.10.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021182
X-RAY DIFFRACTIONr_mcbond_it4.0144.2632876
X-RAY DIFFRACTIONr_mcbond_other4.0124.2632875
X-RAY DIFFRACTIONr_mcangle_it5.4056.3643588
LS refinement shellResolution: 2.021→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 175 -
Rwork0.26 3210 -
all-3385 -
obs--99.12 %

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