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- PDB-3c4v: Structure of the retaining glycosyltransferase MshA:The first ste... -

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Basic information

Entry
Database: PDB / ID: 3c4v
TitleStructure of the retaining glycosyltransferase MshA:The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum : Complex with UDP and 1L-INS-1-P.
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
L-MYO-INOSITOL-1-PHOSPHATE / URIDINE-5'-DIPHOSPHATE / D-inositol 3-phosphate glycosyltransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: 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)94,7007
Polymers93,5852
Non-polymers1,1155
Water1,26170
1
A: Predicted glycosyltransferases
hetero molecules

A: Predicted glycosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4426
Polymers93,5852
Non-polymers8574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4070 Å2
ΔGint-47.7 kcal/mol
Surface area30660 Å2
MethodPISA
2
B: Predicted glycosyltransferases
hetero molecules

B: Predicted glycosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9588
Polymers93,5852
Non-polymers1,3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area5270 Å2
ΔGint-42.8 kcal/mol
Surface area30310 Å2
MethodPISA
3
A: Predicted glycosyltransferases
B: Predicted glycosyltransferases
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)757,59856
Polymers748,67816
Non-polymers8,92040
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 area60210 Å2
ΔGint-356.6 kcal/mol
Surface area221010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.940, 223.940, 125.005
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) / 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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-LIP / L-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 4.19 Å3/Da / Density % sol: 70.62 %
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: Optics 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: 2.6→80 Å / Num. all: 48553 / Num. obs: 48553 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 23
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4 / Num. unique all: 7040 / Rsym value: 0.309 / % possible all: 100

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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 3C4Q

3c4q


Resolution: 2.6→79.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.402 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.271 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21304 2463 5.1 %RANDOM
Rwork0.19005 ---
all0.19122 46089 --
obs0.19122 46089 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.585 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.6→79.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 68 70 6189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9728501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9855780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79923.38284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03415994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1561558
X-RAY DIFFRACTIONr_chiral_restr0.110.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024750
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24221
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.54013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01826295
X-RAY DIFFRACTIONr_scbond_it1.61432498
X-RAY DIFFRACTIONr_scangle_it2.6614.52206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 179 -
Rwork0.298 3412 -
obs--99.94 %

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