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- PDB-6hki: Crystal structure of surface entropy mutant of human O-GlcNAc hyd... -

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Basic information

Entry
Database: PDB / ID: 6hki
TitleCrystal structure of surface entropy mutant of human O-GlcNAc hydrolase
ComponentsProtein O-GlcNAcase
KeywordsHYDROLASE / O-GlcNAc / deglycosylation / glycosidase
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 / Resolution: 3.3 Å
AuthorsMales, A. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structural studies of a surface-entropy reduction mutant of O-GlcNAcase.
Authors: Males, A. / Davies, G.J.
History
DepositionSep 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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


Theoretical massNumber of molelcules
Total (without water)205,8102
Polymers205,8102
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-54 kcal/mol
Surface area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.168, 222.168, 72.396
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 102904.828 Da / Num. of mol.: 2 / Mutation: E602A, E605A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60502, protein O-GlcNAcase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium citrate tribasic, 17% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 3.3→192.4 Å / Num. obs: 31103 / % possible obs: 99.8 % / Redundancy: 16.8 % / Biso Wilson estimate: 58.53 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.11 / Net I/σ(I): 7.3
Reflection shellResolution: 3.3→3.3 Å / Redundancy: 17.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4440 / CC1/2: 0.67 / Rpim(I) all: 0.62 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementStarting model: 5M7R

5m7r


Resolution: 3.3→192.4 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.903 / SU B: 21.085 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23358 1483 4.8 %RANDOM
Rwork0.16914 ---
obs0.17222 29581 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.607 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-0.66 Å2-0 Å2
2---1.31 Å20 Å2
3---4.25 Å2
Refinement stepCycle: 1 / Resolution: 3.3→192.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7865 0 0 1 7866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0148097
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177158
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.65310985
X-RAY DIFFRACTIONr_angle_other_deg0.9251.62516762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1885974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02221.991432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.705151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0021552
X-RAY DIFFRACTIONr_chiral_restr0.0750.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029062
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021610
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_mcbond_it6.0867.3553902
X-RAY DIFFRACTIONr_mcbond_other6.0637.3553901
X-RAY DIFFRACTIONr_mcangle_it9.45611.0064868
X-RAY DIFFRACTIONr_mcangle_other9.45911.0074869
X-RAY DIFFRACTIONr_scbond_it6.027.5134195
X-RAY DIFFRACTIONr_scbond_other6.0197.5144196
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.23711.1276116
X-RAY DIFFRACTIONr_long_range_B_refined12.35683.5119251
X-RAY DIFFRACTIONr_long_range_B_other12.35783.529252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 130 -
Rwork0.284 2133 -
obs--99.74 %

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