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- PDB-5tke: Crystal Structure of Eukaryotic Hydrolase -

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Basic information

Entry
Database: PDB / ID: 5tke
TitleCrystal Structure of Eukaryotic Hydrolase
ComponentsO-GlcNAcase: chimera construct
KeywordsHYDROLASE
Function / homology
Function and homology information


glycoprotein metabolic process / hyalurononglucosaminidase activity / 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 ...glycoprotein metabolic process / hyalurononglucosaminidase activity / 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 / membrane / identical protein binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.481 Å
AuthorsLi, B. / Jiang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
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
DepositionOct 6, 2016Deposition 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: O-GlcNAcase: chimera construct
B: O-GlcNAcase: chimera construct


Theoretical massNumber of molelcules
Total (without water)115,6472
Polymers115,6472
Non-polymers00
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-40 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.060, 96.576, 89.282
Angle α, β, γ (deg.)90.00, 115.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein O-GlcNAcase: chimera construct / 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 60-542; unp residues 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, ...Details: 0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, and 5% w/v polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 44255 / % possible obs: 100 % / Redundancy: 6.4 % / Net I/σ(I): 19.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cbj

2cbj


Resolution: 2.481→44.249 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 2013 4.92 %
Rwork0.1811 --
obs0.1838 40939 91.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.481→44.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6905 0 0 384 7289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017088
X-RAY DIFFRACTIONf_angle_d1.1269587
X-RAY DIFFRACTIONf_dihedral_angle_d18.4524198
X-RAY DIFFRACTIONf_chiral_restr0.0581013
X-RAY DIFFRACTIONf_plane_restr0.0091212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4814-2.54340.3368620.23551344X-RAY DIFFRACTION45
2.5434-2.61220.29511050.23551842X-RAY DIFFRACTION62
2.6122-2.6890.29071300.22622378X-RAY DIFFRACTION79
2.689-2.77580.27181350.22092939X-RAY DIFFRACTION97
2.7758-2.8750.28521480.20163043X-RAY DIFFRACTION100
2.875-2.99010.26841670.1963020X-RAY DIFFRACTION100
2.9901-3.12610.24961720.2013017X-RAY DIFFRACTION100
3.1261-3.29090.27071500.21013045X-RAY DIFFRACTION100
3.2909-3.4970.26481550.19123034X-RAY DIFFRACTION100
3.497-3.76690.25551590.17133034X-RAY DIFFRACTION100
3.7669-4.14570.21031500.15543045X-RAY DIFFRACTION100
4.1457-4.7450.1821510.13683054X-RAY DIFFRACTION100
4.745-5.97590.21511510.16783086X-RAY DIFFRACTION100
5.9759-44.25640.20641780.18523045X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -16.201 Å / Origin y: -63.9248 Å / Origin z: 97.0115 Å
111213212223313233
T0.222 Å20.0098 Å2-0.0061 Å2-0.3625 Å20.0326 Å2--0.2219 Å2
L1.1517 °2-0.1645 °2-0.3249 °2-1.2829 °20.1398 °2--1.0859 °2
S0.0027 Å °0.3129 Å °-0.0108 Å °0.046 Å °0.046 Å °0.0696 Å °-0.0431 Å °-0.3953 Å °-0.0395 Å °
Refinement TLS groupSelection details: all

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