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- PDB-7ou8: Human O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines -

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Basic information

Entry
Database: PDB / ID: 7ou8
TitleHuman O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines
ComponentsO-GlcNAcase BT_4395
KeywordsHYDROLASE / Carbohydrate / Inhibitor / Probe / N-acetylglucosamine
Function / homology
Function and homology information


protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding
Similarity search - Function
: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 ...: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-1XI / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMales, A. / Davies, G.J. / Gonzalez-Cuesta, M. / Mellet, C.O. / Fernandez, J.M.G. / Sidhu, P. / Ashmus, R. / Busmann, J. / Vocadlo, D.J. / Foster, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Bicyclic Picomolar OGA Inhibitors Enable Chemoproteomic Mapping of Its Endogenous Post-translational Modifications
Authors: Gonzalez-Cuesta, M. / Sidhu, P. / Ashmus, R.A. / Males, A. / Proceviat, C. / Madden, Z. / Rogalski, J.C. / Busmann, J.A. / Foster, L.J. / Garcia Fernandez, J.M. / Davies, G.J. / Ortiz Mellet, C. / Vocadlo, D.J.
History
DepositionJun 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: O-GlcNAcase BT_4395
BBB: O-GlcNAcase BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,9496
Polymers169,1762
Non-polymers7734
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12 kcal/mol
Surface area57610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.530, 160.621, 224.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein O-GlcNAcase BT_4395 / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Hexosaminidase B ...Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Hexosaminidase B / N-acetyl-beta-glucosaminidase


Mass: 84587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89ZI2, protein O-GlcNAcase
#2: Chemical ChemComp-1XI / ~{N}-[(3~{Z},6~{S},7~{R},8~{R},8~{a}~{S})-7,8-bis(oxidanyl)-3-(phenylmethyl)imino-1,5,6,7,8,8~{a}-hexahydro-[1,3]thiazolo[3,4-a]pyridin-6-yl]ethanamide


Mass: 335.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.14 - 0.2 M triammonium citrate pH 7.5, 16-20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.5→75.62 Å / Num. obs: 298134 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.027 / Rrim(I) all: 0.076 / Net I/σ(I): 12.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 14662 / CC1/2: 0.65 / Rpim(I) all: 0.371 / Rrim(I) all: 0.896 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M7R

5m7r


Resolution: 1.5→75.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.983 / SU ML: 0.068 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2316 14864 4.988 %
Rwork0.2089 283143 -
all0.21 --
obs-298007 99.951 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0 Å20 Å2
2--1.889 Å2-0 Å2
3----0.829 Å2
Refinement stepCycle: LAST / Resolution: 1.5→75.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11260 0 51 896 12207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311899
X-RAY DIFFRACTIONr_bond_other_d0.0030.01710970
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.64616211
X-RAY DIFFRACTIONr_angle_other_deg1.5131.57725293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05151491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86723.638624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.792151975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031553
X-RAY DIFFRACTIONr_chiral_restr0.0880.21540
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022766
X-RAY DIFFRACTIONr_nbd_refined0.2210.22395
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.210409
X-RAY DIFFRACTIONr_nbtor_refined0.1750.25671
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.25055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2714
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.23
X-RAY DIFFRACTIONr_metal_ion_refined0.190.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.216
X-RAY DIFFRACTIONr_nbd_other0.2150.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.233
X-RAY DIFFRACTIONr_mcbond_it2.4942.7115812
X-RAY DIFFRACTIONr_mcbond_other2.4942.715811
X-RAY DIFFRACTIONr_mcangle_it3.474.0537281
X-RAY DIFFRACTIONr_mcangle_other3.4694.0547282
X-RAY DIFFRACTIONr_scbond_it2.9172.8286087
X-RAY DIFFRACTIONr_scbond_other2.9172.8286088
X-RAY DIFFRACTIONr_scangle_it4.3554.1458905
X-RAY DIFFRACTIONr_scangle_other4.3554.1458906
X-RAY DIFFRACTIONr_lrange_it5.630.43113561
X-RAY DIFFRACTIONr_lrange_other5.630.4313561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.42411000.40420702X-RAY DIFFRACTION99.8489
1.539-1.5810.36710750.36520204X-RAY DIFFRACTION100
1.581-1.6270.31910740.32419672X-RAY DIFFRACTION100
1.627-1.6770.29610060.2919128X-RAY DIFFRACTION100
1.677-1.7320.2889720.26318551X-RAY DIFFRACTION100
1.732-1.7930.2819410.24117954X-RAY DIFFRACTION100
1.793-1.860.2648940.23117336X-RAY DIFFRACTION100
1.86-1.9360.2368920.21216683X-RAY DIFFRACTION100
1.936-2.0230.2377910.20416087X-RAY DIFFRACTION99.9882
2.023-2.1210.2248000.20115375X-RAY DIFFRACTION99.9938
2.121-2.2360.2248260.19114587X-RAY DIFFRACTION100
2.236-2.3720.2097510.18313791X-RAY DIFFRACTION100
2.372-2.5350.2186750.18713046X-RAY DIFFRACTION100
2.535-2.7380.2376230.18412199X-RAY DIFFRACTION100
2.738-30.2075430.18211271X-RAY DIFFRACTION100
3-3.3540.2225150.1910222X-RAY DIFFRACTION100
3.354-3.8720.1975010.1899023X-RAY DIFFRACTION100
3.872-4.7420.173840.1547749X-RAY DIFFRACTION100
4.742-6.7050.2182990.1926070X-RAY DIFFRACTION99.9529
6.705-75.620.1882020.23493X-RAY DIFFRACTION99.757

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