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- PDB-3c4q: Structure of the retaining glycosyltransferase MshA : The first s... -

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Basic information

Entry
Database: PDB / ID: 3c4q
TitleStructure of the retaining glycosyltransferase MshA : The first step in mycothiol biosynthesis. Organism : Corynebacterium glutamicum- Complex with UDP
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
URIDINE-5'-DIPHOSPHATE / D-inositol 3-phosphate glycosyltransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 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 / 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 / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Assembly

Deposited unit
A: Predicted glycosyltransferases
B: Predicted glycosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6348
Polymers93,5852
Non-polymers1,0496
Water99155
1
A: Predicted glycosyltransferases
hetero molecules

A: Predicted glycosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6348
Polymers93,5852
Non-polymers1,0496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4480 Å2
ΔGint-74.4 kcal/mol
Surface area30590 Å2
MethodPISA
2
B: Predicted glycosyltransferases
hetero molecules

B: Predicted glycosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6348
Polymers93,5852
Non-polymers1,0496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area4490 Å2
ΔGint-73.9 kcal/mol
Surface area31000 Å2
MethodPISA
3
A: Predicted glycosyltransferases
B: Predicted glycosyltransferases
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)757,07064
Polymers748,67816
Non-polymers8,39248
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area58700 Å2
ΔGint-597.5 kcal/mol
Surface area223550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.245, 224.245, 125.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Predicted glycosyltransferases


Mass: 46792.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: MshA / Plasmid: pET29 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NTA6, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: Protein (40 mg/ml, 400 mM Ammonium sulfate, 10% glycerol, 0.5 mM EDTA, 1 mM BME, 10 mM UDPNAG) Precipitant (0.8 M sodium citrate pH 5.5 ), Vapor diffusion under oil, temperature 298K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2007
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes
RadiationMonochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.8→80 Å / Num. all: 37594 / Num. obs: 37594 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 69.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5474 / Rsym value: 0.318 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C48

3c48


Resolution: 2.8→78.25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.121 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.4 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21754 1885 5 %RANDOM
Rwork0.18379 ---
all0.18547 35709 --
obs0.18547 35709 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.568 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→78.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 62 55 6168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226257
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.978527
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3635786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52923.357286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.46315999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2041558
X-RAY DIFFRACTIONr_chiral_restr0.1690.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.22868
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24242
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3290.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.621.53999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10726313
X-RAY DIFFRACTIONr_scbond_it1.73632508
X-RAY DIFFRACTIONr_scangle_it2.9434.52211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 157 -
Rwork0.286 2600 -
obs--96.2 %
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)
10.6777-0.19230.15831.3584-0.30732.0161-0.0028-0.1174-0.0109-0.00790.03590.05070.08290.0879-0.03310.12270.0393-0.00370.13490.0242-0.291361.79846.7510.9
23.17980.4977-0.38252.60350.22573.1807-0.0228-0.15420.11640.03170.0063-0.0534-0.28950.17210.01640.01130.01520.0280.18640.008-0.364489.87651.0120.899
32.16160.1113-0.06370.48030.18642.05580.04050.3068-0.2293-0.0213-0.0076-0.01560.041-0.1582-0.0328-0.0606-0.0036-0.00440.2788-0.0596-0.2588101.41630.663-11.001
43.3758-0.3174-0.53873.79140.58962.59240.00130.09310.0977-0.19280.1649-0.1648-0.26880.3315-0.16630.0259-0.07210.02990.192-0.0629-0.383484.25453.027-21.288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 195
2X-RAY DIFFRACTION1A386 - 409
3X-RAY DIFFRACTION2A196 - 385
4X-RAY DIFFRACTION3B1 - 195
5X-RAY DIFFRACTION3B386 - 409
6X-RAY DIFFRACTION4B196 - 385

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