[English] 日本語
Yorodumi
- PDB-5un9: The crystal structure of human O-GlcNAcase in complex with Thiamet-G -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5un9
TitleThe crystal structure of human O-GlcNAcase in complex with Thiamet-G
ComponentsProtein O-GlcNAcase
KeywordsHYDROLASE / Human O-GlcNAcase / Thiemat-G
Function / homology
Function and homology information


hyalurononglucosaminidase activity / glycoprotein metabolic process / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein O-linked glycosylation / protein deglycosylation ...hyalurononglucosaminidase activity / glycoprotein metabolic process / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein O-linked glycosylation / protein deglycosylation / beta-N-acetylglucosaminidase activity / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Acyl-CoA N-acyltransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NHT / Protein O-GlcNAcase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, B. / Jiang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Wisconsin-Madison United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structures of human O-GlcNAcase and its complexes reveal a new substrate recognition mode.
Authors: Li, B. / Li, H. / Lu, L. / Jiang, J.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein O-GlcNAcase
B: Protein O-GlcNAcase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1444
Polymers115,6472
Non-polymers4972
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-36 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.572, 96.106, 89.534
Angle α, β, γ (deg.)90.00, 115.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein O-GlcNAcase / OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma- ...OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma-expressed antigen 5 / N-acetyl-beta-D-glucosaminidase / N-acetyl-beta-glucosaminidase / Nuclear cytoplasmic O-GlcNAcase and acetyltransferase / NCOAT


Mass: 57823.566 Da / Num. of mol.: 2 / Fragment: UNP residues 60-400 and 553-704
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-NHT / (3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL


Mass: 248.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.128 M potassium thiocyanate, 0.032 M ammonium citrate tribasic (pH 7.0), 0.016 M imidazole (pH 7.0), 0.002 M zinc sulfate heptahydrate, 0.02 M MES monohydrate (pH 6.5), 12.8% w/v ...Details: 0.128 M potassium thiocyanate, 0.032 M ammonium citrate tribasic (pH 7.0), 0.016 M imidazole (pH 7.0), 0.002 M zinc sulfate heptahydrate, 0.02 M MES monohydrate (pH 6.5), 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, 5% v/v polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 44310 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 23
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2106 / CC1/2: 0.785 / Rpim(I) all: 0.278 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKE

5tke


Resolution: 2.5→29.797 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.96
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 2107 5.01 %Random
Rwork0.2103 ---
obs0.2127 42091 94.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 32 238 7192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117141
X-RAY DIFFRACTIONf_angle_d1.2119665
X-RAY DIFFRACTIONf_dihedral_angle_d18.8084217
X-RAY DIFFRACTIONf_chiral_restr0.0651025
X-RAY DIFFRACTIONf_plane_restr0.0081221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4904-2.54830.3214820.25141504X-RAY DIFFRACTION54
2.5483-2.6120.33861070.262055X-RAY DIFFRACTION73
2.612-2.68260.30441390.24422665X-RAY DIFFRACTION95
2.6826-2.76150.28981510.24352772X-RAY DIFFRACTION99
2.7615-2.85060.28611510.23922815X-RAY DIFFRACTION100
2.8506-2.95240.30781330.23472808X-RAY DIFFRACTION100
2.9524-3.07040.30721510.23182809X-RAY DIFFRACTION100
3.0704-3.210.25631530.22742801X-RAY DIFFRACTION100
3.21-3.37910.28251550.21892779X-RAY DIFFRACTION100
3.3791-3.59040.24731320.21072830X-RAY DIFFRACTION100
3.5904-3.86710.25531520.20852811X-RAY DIFFRACTION100
3.8671-4.25530.24291410.19382819X-RAY DIFFRACTION100
4.2553-4.86870.2091500.17592822X-RAY DIFFRACTION100
4.8687-6.12530.25361640.19362805X-RAY DIFFRACTION100
6.1253-29.79910.23931460.19642889X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 121.2206 Å / Origin y: 11.7123 Å / Origin z: -56.4994 Å
111213212223313233
T0.1609 Å2-0.0137 Å2-0.014 Å2-0.2699 Å2-0.0242 Å2--0.1508 Å2
L1.0087 °20.0952 °2-0.3956 °2-0.8592 °2-0.0005 °2--1.0034 °2
S-0.041 Å °-0.3559 Å °-0.0071 Å °-0.1069 Å °0.0813 Å °-0.0251 Å °-0.0443 Å °0.4678 Å °-0.0221 Å °
Refinement TLS groupSelection details: all

+
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