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- PDB-4ais: A complex structure of BtGH84 -

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Basic information

Entry
Database: PDB / ID: 4ais
TitleA complex structure of BtGH84
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


protein O-GlcNAcase / protein deglycosylation / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding
Similarity search - Function
: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Chitobiase/beta-hexosaminidase domain 2-like ...: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLYCOLIC ACID / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHe, Y. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Metabolism of Vertebrate Amino Sugars with N-Glycolyl Groups: Intracellular Beta-O-Linked N-Glycolylglucosamine (Glcngc), Udp-Glcngc, and the Biochemical and Structural Rationale for the ...Title: Metabolism of Vertebrate Amino Sugars with N-Glycolyl Groups: Intracellular Beta-O-Linked N-Glycolylglucosamine (Glcngc), Udp-Glcngc, and the Biochemical and Structural Rationale for the Substrate Tolerance of Beta-O-Linked Beta-N-Acetylglucosaminidase.
Authors: Macauley, M.S. / Chan, J. / Zandberg, W.F. / He, Y. / Whitworth, G.E. / Stubbs, K.A. / Yuzwa, S.A. / Bennet, A.J. / Varki, A. / Davies, G.J. / Vocadlo, D.J.
History
DepositionFeb 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-GLCNACASE BT_4395
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,6047
Polymers169,1762
Non-polymers4285
Water15,475859
1
A: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7563
Polymers84,5881
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8484
Polymers84,5881
Non-polymers2603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.330, 93.770, 99.160
Angle α, β, γ (deg.)104.27, 94.01, 102.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein O-GLCNACASE BT_4395 / BTGH84 / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE GH84 / HEXOSAMINIDASE B / N-ACETYL-BETA- ...BTGH84 / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE GH84 / 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 VPI-5482 (bacteria)
Plasmid: YSBLLICPET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase, protein O-GlcNAcase
#2: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 2.72 Å3/Da / Density % sol: 54.88 % / Description: NONE
Crystal growDetails: 0.3 M AMMONIUM ACETATE, 0.1 M MES PH 6.0, 15% PEG 3350(W/V), 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→34.38 Å / Num. obs: 113272 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHO

2cho


Resolution: 2→33.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.533 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24406 5687 5 %RANDOM
Rwork0.19339 ---
obs0.19594 107583 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.549 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0.26 Å2-0.57 Å2
2--0.41 Å2-1.71 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10367 0 28 859 11254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.95514560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43951286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76924.849530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8651551
X-RAY DIFFRACTIONr_chiral_restr0.1090.21541
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218230
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 374 -
Rwork0.285 7970 -
obs--95.81 %

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