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- PDB-3mbo: Crystal Structure of the Glycosyltransferase BaBshA bound with UD... -

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Basic information

Entry
Database: PDB / ID: 3mbo
TitleCrystal Structure of the Glycosyltransferase BaBshA bound with UDP and L-malate
ComponentsGlycosyltransferase, group 1 family
KeywordsTRANSFERASE / glycosyltransferase / bacillus anthracis / UDP / L-malate
Function / homology
Function and homology information


bacillithiol biosynthetic process / UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid 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
D-MALATE / URIDINE-5'-DIPHOSPHATE / N-acetyl-alpha-D-glucosaminyl L-malate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.307 Å
AuthorsWallace, B.D. / Claiborne, A. / Redinbo, M.R.
CitationJournal: Biochemistry / Year: 2010
Title: Characterization of the N-Acetyl-alpha-d-glucosaminyl l-Malate Synthase and Deacetylase Functions for Bacillithiol Biosynthesis in Bacillus anthracis
Authors: Parsonage, D. / Newton, G.L. / Holder, R.C. / Wallace, B.D. / Paige, C. / Dos Santos, P.C. / Redinbo, M.R. / Fahey, R.C. / Reid, S.D. / Claiborne, A.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase, group 1 family
B: Glycosyltransferase, group 1 family
C: Glycosyltransferase, group 1 family
D: Glycosyltransferase, group 1 family
E: Glycosyltransferase, group 1 family
F: Glycosyltransferase, group 1 family
G: Glycosyltransferase, group 1 family
H: Glycosyltransferase, group 1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,03239
Polymers370,8978
Non-polymers4,13631
Water5,188288
1
A: Glycosyltransferase, group 1 family
B: Glycosyltransferase, group 1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,90711
Polymers92,7242
Non-polymers1,1839
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-38 kcal/mol
Surface area29410 Å2
MethodPISA
2
C: Glycosyltransferase, group 1 family
D: Glycosyltransferase, group 1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,74710
Polymers92,7242
Non-polymers1,0238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-48 kcal/mol
Surface area30090 Å2
MethodPISA
3
E: Glycosyltransferase, group 1 family
F: Glycosyltransferase, group 1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,02313
Polymers92,7242
Non-polymers1,29911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-46 kcal/mol
Surface area29570 Å2
MethodPISA
4
G: Glycosyltransferase, group 1 family
H: Glycosyltransferase, group 1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3555
Polymers92,7242
Non-polymers6303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-34 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.266, 226.266, 75.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsGEL FILTRATION EXPERIMENT SHOWS THAT THE BIOLOGICAL UNIT IS DIMER.

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Glycosyltransferase, group 1 family / Glycosyl transferase / group 1 family protein


Mass: 46362.086 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: K-12 / Gene: BaBshA, BAS1445, BA_1558, GBAA1558, GBAA_1558 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q81ST7

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Non-polymers , 5 types, 319 molecules

#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 0.2 M MgFormate, 0.02% sodium azide, 1 mM L-malate, 1 mM Uridine diphosphate, pH 7.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 57310 / % possible obs: 99.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3.3-3.362.70.91993.7
3.36-3.423.20.81996.2
3.42-3.483.60.76397.5
3.48-3.554.10.59799.4
3.55-3.634.40.535100
3.63-3.724.70.464100
3.72-3.814.90.381100
3.81-3.915.10.368100
3.91-4.035.40.254100
4.03-4.165.70.227100
4.16-4.3160.201100
4.31-4.486.20.17100
4.48-4.686.50.153100
4.68-4.936.80.146100
4.93-5.247.10.148100
5.24-5.647.40.162100
5.64-6.217.50.158100
6.21-7.17.60.129100
7.1-8.947.50.085100
8.94-507.20.085100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJM

2jjm


Resolution: 3.307→48.222 Å / Occupancy max: 1 / Occupancy min: 0.75 / SU ML: 3.28 / σ(F): 0.08 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2770 5.11 %
Rwork0.2278 --
obs0.2293 54222 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.359 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 74.394 Å2
Baniso -1Baniso -2Baniso -3
1--4.606 Å2-0 Å20 Å2
2---4.606 Å20 Å2
3---7.722 Å2
Refinement stepCycle: LAST / Resolution: 3.307→48.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23328 0 264 288 23880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923967
X-RAY DIFFRACTIONf_angle_d1.9732403
X-RAY DIFFRACTIONf_dihedral_angle_d19.1438781
X-RAY DIFFRACTIONf_chiral_restr0.1343757
X-RAY DIFFRACTIONf_plane_restr0.0074123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3068-3.36380.35351060.30632035X-RAY DIFFRACTION75
3.3638-3.42490.3381360.31852161X-RAY DIFFRACTION79
3.4249-3.49080.33071370.29992204X-RAY DIFFRACTION84
3.4908-3.5620.31861350.27452418X-RAY DIFFRACTION89
3.562-3.63940.26241250.25822416X-RAY DIFFRACTION89
3.6394-3.72410.27481400.24742516X-RAY DIFFRACTION92
3.7241-3.81710.27531680.25082479X-RAY DIFFRACTION93
3.8171-3.92030.33321350.24582572X-RAY DIFFRACTION94
3.9203-4.03560.26171360.21842595X-RAY DIFFRACTION95
4.0356-4.16580.20641200.21552677X-RAY DIFFRACTION97
4.1658-4.31460.23581180.20462657X-RAY DIFFRACTION98
4.3146-4.48720.2461470.20092703X-RAY DIFFRACTION99
4.4872-4.69130.2331340.19842723X-RAY DIFFRACTION99
4.6913-4.93840.25361420.19482723X-RAY DIFFRACTION99
4.9384-5.24740.21941500.19222709X-RAY DIFFRACTION99
5.2474-5.6520.24831530.21072708X-RAY DIFFRACTION99
5.652-6.21980.24921580.22452714X-RAY DIFFRACTION99
6.2198-7.11730.24251370.21912759X-RAY DIFFRACTION99
7.1173-8.95770.1971380.18132794X-RAY DIFFRACTION100
8.9577-48.22740.20061550.19162889X-RAY DIFFRACTION100

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