[English] 日本語
Yorodumi
- PDB-3c48: Structure of the retaining glycosyltransferase MshA: The first st... -

+
Open data


ID or keywords:

Loading...

-
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 / UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more