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- PDB-5un9: The crystal structure of human O-GlcNAcase in complex with Thiamet-G -

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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


glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding ...glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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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

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