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- PDB-2xsb: OgOGA PUGNAc complex -

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Basic information

Entry
Database: PDB / ID: 2xsb
TitleOgOGA PUGNAc complex
ComponentsHYALURONOGLUCOSAMINIDASE
KeywordsHYDROLASE / O-GLCNACYLATION / O-GLCNACASE / GLYCOSYL HYDROLASE
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
Similarity search - Function
STAT; domain 1 / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...STAT; domain 1 / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone / Protein O-GlcNAcase
Similarity search - Component
Biological speciesOCEANICOLA GRANULOSUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsSchuttelkopf, A.W. / van Aalten, D.M.F.
CitationJournal: Biochem.J. / Year: 2010
Title: Human Oga Binds Substrates in a Conserved Peptide Recognition Groove.
Authors: Schimpl, M. / Schuttelkopf, A.W. / Borodkin, V.S. / Van Aalten, D.M.F.
History
DepositionSep 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYALURONOGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3533
Polymers50,0991
Non-polymers2552
Water1,36976
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.583, 96.289, 59.973
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2058-

HOH

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Components

#1: Protein HYALURONOGLUCOSAMINIDASE


Mass: 50098.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) OCEANICOLA GRANULOSUS (bacteria) / Strain: HTCC2516 / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2CEE3, beta-N-acetylhexosaminidase
#2: Sugar ChemComp-GDL / 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone / 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE


Type: D-saccharide / Mass: 219.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5
Details: 18% POLYETHYLENE GLYCOL 4000, 100-250 MM MGCL2, 100 MM TRIS/HCL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 26338 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XSA

2xsa


Resolution: 2.11→19.99 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.184 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27819 653 2.5 %RANDOM
Rwork0.24167 ---
obs0.24259 25600 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.875 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å2-0.9 Å2
2--3.11 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.11→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 16 76 3386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223398
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9544645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03222.515163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77115482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5521535
X-RAY DIFFRACTIONr_chiral_restr0.0860.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212689
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6231.52117
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14923380
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64831281
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7434.51265
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.108→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 24 -
Rwork0.33 1545 -
obs--100 %

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