[English] 日本語
Yorodumi
- PDB-7ec3: Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ec3
TitleCrystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)
Components
  • 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
  • Glycosyl transferase, group 1 family protein
KeywordsTRANSFERASE / Glycosylation
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding / cytoplasm
Similarity search - Function
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 / Glycosyl transferase, group 1 family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, D.-G. / Baek, I. / Lee, Y. / Kim, H.S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1C1C1009512 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017R1C1B2012225 Korea, Republic Of
National Research Foundation (NRF, Korea)2015R1D1A4A01020265 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins.
Authors: Kim, D.G. / Baek, I. / Lee, Y. / Kim, H. / Kim, J.Y. / Bang, G. / Kim, S. / Yoon, H.J. / Han, B.W. / Suh, S.W. / Kim, H.S.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl transferase, group 1 family protein
C: Glycosyl transferase, group 1 family protein
D: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
G: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,83011
Polymers120,9164
Non-polymers1,9147
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint6 kcal/mol
Surface area44090 Å2
Unit cell
Length a, b, c (Å)70.201, 130.568, 189.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glycosyl transferase, group 1 family protein


Mass: 59631.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: SAUSA300_0550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XGN0
#2: Protein/peptide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE


Mass: 826.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 20 mM CaCl2, 85 mM tri-sodium citrate at pH 5.6, 25.5% (w/v) PEG 4,000, and 15% (w/v) glycerol for the SdgB crystal soaked with the 2.66 mM 9mer SD-repeat peptide and 9.60 mM UDP-GlcNAc

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 60708 / % possible obs: 96.7 % / Redundancy: 5.4 % / CC1/2: 0.934 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2941 / CC1/2: 0.776

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EC1

7ec1


Resolution: 2.5→47.05 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.08 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3041 5 %RANDOM
Rwork0.191 ---
obs0.193 57606 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.14 Å2 / Biso mean: 38.96 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--4.83 Å20 Å2
3----3.06 Å2
Refinement stepCycle: final / Resolution: 2.5→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8433 0 122 24 8579
Biso mean--37 30.01 -
Num. residues----1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177974
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.67911885
X-RAY DIFFRACTIONr_angle_other_deg1.2471.58818344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4175998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76722.908502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.141151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8261546
X-RAY DIFFRACTIONr_chiral_restr0.080.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

+
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://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