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- PDB-6r45: Crystal structure of eukaryotic O-GlcNAcase HAT-like domain -

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Basic information

Entry
Database: PDB / ID: 6r45
TitleCrystal structure of eukaryotic O-GlcNAcase HAT-like domain
ComponentsO-GlcNAcase
KeywordsTRANSFERASE / O-GlcNAcase / Eukaryote / acetyltransferase / Trichoplax adhaerens
Function / homology
Function and homology information


glycoprotein metabolic process / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / beta-N-acetylglucosaminidase activity
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesTrichoplax adhaerens (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.784 Å
AuthorsRaimi, O.G. / Gorelik, A. / Hopkins-Navratilova, I. / Aristotelous, T. / Ferenbach, A. / vanAalten, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of eukaryotic O-GlcNAcase HAT-like domain
Authors: Raimi, O.G. / Gorelik, A.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,7893
Polymers49,6662
Non-polymers1221
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint0 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.250, 43.520, 59.840
Angle α, β, γ (deg.)87.52, 85.24, 87.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein O-GlcNAcase


Mass: 24833.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5X2Y8, protein O-GlcNAcase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES 7.5, 60 mM Sodium potassium-tartrate and 27.5 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.784→59.59 Å / Num. obs: 36731 / % possible obs: 89 % / Redundancy: 1.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 1.784→1.848 Å / Num. unique obs: 3663

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMH

4bmh


Resolution: 1.784→36.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.146 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23979 775 2.1 %RANDOM
Rwork0.19257 ---
obs0.19351 35956 88.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-1.5 Å20.28 Å2
2--0.42 Å2-0.45 Å2
3----1.36 Å2
Refinement stepCycle: 1 / Resolution: 1.784→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3388 0 8 170 3566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173182
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6484738
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5787395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5735414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17921.707205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29315618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9881528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02782
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_it1.8872.1691642
X-RAY DIFFRACTIONr_mcbond_other1.8862.1691640
X-RAY DIFFRACTIONr_mcangle_it2.7983.2462048
X-RAY DIFFRACTIONr_mcangle_other2.7973.2472049
X-RAY DIFFRACTIONr_scbond_it2.5662.481854
X-RAY DIFFRACTIONr_scbond_other2.5652.481855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.043.5992687
X-RAY DIFFRACTIONr_long_range_B_refined5.39825.6754099
X-RAY DIFFRACTIONr_long_range_B_other5.39225.6254078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.784→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 63 -
Rwork0.246 2655 -
obs--88.68 %

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