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- PDB-3c48: Structure of the retaining glycosyltransferase MshA: The first st... -

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Basic information

Entry
Database: PDB / ID: 3c48
TitleStructure of the retaining glycosyltransferase MshA: The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum- APO (OPEN) structure.
ComponentsPredicted glycosyltransferases
KeywordsTRANSFERASE / retaining glycosyltransferase / beta alpha beta / substrate assisted catalysis
Function / homology
Function and homology information


D-inositol-3-phosphate glycosyltransferase / D-inositol-3-phosphate glycosyltransferase activity / mycothiol biosynthetic process / acetylglucosaminyltransferase activity / magnesium ion binding
Similarity search - Function
Mycothiol biosynthesis protein, MshA / Glycosyl transferase 4-like domain / 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-inositol 3-phosphate glycosyltransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsVetting, M.W. / Frantom, P.A. / Blanchard, J.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Enzymatic Analysis of MshA from Corynebacterium glutamicum: SUBSTRATE-ASSISTED CATALYSIS
Authors: Vetting, M.W. / Frantom, P.A. / Blanchard, J.S.
History
DepositionJan 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Predicted glycosyltransferases
B: Predicted glycosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,55410
Polymers95,7852
Non-polymers7698
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-122.1 kcal/mol
Surface area33900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.743, 79.743, 148.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Predicted glycosyltransferases


Mass: 47892.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: MshA / Plasmid: pET28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NTA6, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: Protein (15 mg/ml, 400 mM Ammonium sulfate, 10% glycerol, 0.5 mM EDTA, 1 mM BME): Precipitant (20% Peg4000, 100 mM Tris pH 8.5, 200 mm LiSO4), Vapor diffusion under oil, temperature 291K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2007
RadiationMonochromator: MSC Confocal Blue Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. all: 178087 / Num. obs: 60789 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 16.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8239 / Rsym value: 0.238 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→34.53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.904 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.177 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22173 3079 5.1 %RANDOM
Rwork0.18014 ---
all0.18222 57704 --
obs0.18222 57704 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å20 Å2
2---0.19 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6148 0 40 405 6593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216301
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9628572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1635786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31923.425292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.643151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7931557
X-RAY DIFFRACTIONr_chiral_restr0.1120.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024801
X-RAY DIFFRACTIONr_nbd_refined0.1990.22795
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24189
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2441
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.215
X-RAY DIFFRACTIONr_mcbond_it0.8051.54102
X-RAY DIFFRACTIONr_mcangle_it1.2826366
X-RAY DIFFRACTIONr_scbond_it2.08432513
X-RAY DIFFRACTIONr_scangle_it3.1394.52206
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 189 -
Rwork0.219 3689 -
obs--84.19 %
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)
11.5565-0.0070.19671.67670.03010.66580.0999-0.23610.13370.182-0.22140.0532-0.1513-0.01950.1215-0.0788-0.1602-0.0201-0.0252-0.0177-0.1288-16.57837.92922.152
25.38071.4810.41672.9067-0.57222.18640.4413-0.96490.45030.2326-0.36440.27620.0895-0.0363-0.0769-0.1749-0.21230.11760.06-0.1789-0.0415-15.64473.7329.904
31.18780.0585-0.10771.9324-0.36950.47220.114-0.2019-0.14550.1702-0.2174-0.01430.02980.01190.1034-0.1048-0.1824-0.0333-0.00180.0718-0.1344-16.54610.27324.843
42.07750.6182-0.15211.571-0.46721.6138-0.2320.12640.1057-0.17980.1264-0.02640.05980.03730.1056-0.0869-0.0861-0.0322-0.0973-0.0074-0.1667-20.147-23.0339.409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 19521 - 215
2X-RAY DIFFRACTION1AA394 - 418414 - 438
3X-RAY DIFFRACTION2AA196 - 393216 - 413
4X-RAY DIFFRACTION3BB1 - 19521 - 215
5X-RAY DIFFRACTION3BB394 - 418414 - 438
6X-RAY DIFFRACTION4BB196 - 393216 - 413

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