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Basic information

Entry
Database: PDB / ID: 2x0h
TitleBtGH84 Michaelis complex
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / INHIBITOR / GLYCOSIDASE
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 / Hyaluronidase post-catalytic domain-like / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 ...: / : / Carbohydrate binding module family 32 / Bacterial GH84, post-catalytic domain / Hyaluronidase post-catalytic domain-like / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, 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
Chem-14T / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsHe, Y. / Davies, G.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Visualizing the Reaction Coordinate of an O-Glcnac Hydrolase
Authors: He, Y. / Macauley, M.S. / Stubbs, K.A. / Vocadlo, D.J. / Davies, G.J.
History
DepositionDec 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _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: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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. THE SHEETS PRESENTED AS "BB" 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: O-GLCNACASE BT_4395
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,50711
Polymers169,1762
Non-polymers1,3319
Water13,205733
1
A: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1414
Polymers84,5881
Non-polymers5533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3667
Polymers84,5881
Non-polymers7786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.630, 163.147, 224.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein O-GLCNACASE BT_4395 / BETA-HEXOSAMINIDASE / N-ACETYL-BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE ...BETA-HEXOSAMINIDASE / N-ACETYL-BETA-GLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / HEXOSAMINIDASE B / GH84 / BTGH84


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
#2: Sugar ChemComp-14T / 3,4-difluorophenyl 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-glucopyranoside / 3,4-difluorophenyl 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-glucoside / 3,4-difluorophenyl 2-deoxy-2-[(difluoroacetyl)amino]-D-glucoside / 3,4-difluorophenyl 2-deoxy-2-[(difluoroacetyl)amino]-glucoside


Type: D-saccharide / Mass: 369.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H15F4NO6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.96 Å3/Da / Density % sol: 58.41 % / Description: NONE
Crystal growDetails: 0.1M IMIDAZOLE PH 8.0, 10% PEG8000 (W/V), 3% TRIMETHYLAMINE N-OXIDE DIHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 95890 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.4
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHO

2cho


Resolution: 2.21→48.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.07 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22589 4772 5 %RANDOM
Rwork0.1942 ---
obs0.19581 90965 99.21 %-
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: 41.482 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2--4.92 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.21→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10354 0 87 733 11174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9614717
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06351289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88724.776536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.048151883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.531553
X-RAY DIFFRACTIONr_chiral_restr0.1020.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218314
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_it0.6761.56454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.207210461
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.22534404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3934.54254
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: 2.209→2.266 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 342 -
Rwork0.244 6657 -
obs--99.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4556-0.97081.02343.8998-1.08454.1593-0.15540.60950.6079-0.56410.1282-0.2029-0.67890.57160.02720.3693-0.16790.04850.39310.05030.23198.345154.3019-2.8046
21.99820.35960.60190.94380.58092.03370.00070.0282-0.12280.04110.06810.00110.18980.0788-0.06880.11520.03820.01120.0637-0.04440.1107-1.484934.796418.0011
32.2686-0.05521.07121.0875-0.13593.405-0.0093-0.0977-0.13780.23090.0852-0.08880.09230.6812-0.0760.19290.07940.01110.3023-0.11260.154717.855544.069446.1043
42.45240.4192-0.56493.0004-2.02244.925-0.0336-0.2854-0.36590.0802-0.012-0.13880.51290.14830.04560.1990.0157-0.02310.12710.02540.15048.483453.341895.0824
52.2745-0.2583-0.11110.95280.3391.7829-0.0533-0.0170.2204-0.01710.05610.0679-0.2018-0.0173-0.00270.1428-0.0329-0.02280.01580.00270.1323-1.20273.929874.1564
62.1564-0.1051-0.69081.69290.12393.5703-0.07730.36920.0935-0.31020.2018-0.1467-0.1990.6263-0.12450.2127-0.1317-0.0120.2901-0.06770.131617.845264.543146.3847
76.2506-1.1245-1.695.0442-0.42045.8526-0.1936-0.4631-0.57760.15880.15020.27370.7065-0.1740.04340.53980.10750.09920.17820.08440.4839-2.697728.103455.8577
810.9073-0.29940.1257.4816-1.87926.6925-0.12090.63570.65490.31090.21040.3658-0.8494-0.4779-0.08940.8004-0.0538-0.01330.33150.10910.4406-2.039979.277133.7322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 128
2X-RAY DIFFRACTION2A129 - 459
3X-RAY DIFFRACTION2A1000
4X-RAY DIFFRACTION3A460 - 593
5X-RAY DIFFRACTION4B4 - 128
6X-RAY DIFFRACTION4B1716
7X-RAY DIFFRACTION5B129 - 459
8X-RAY DIFFRACTION5B1000
9X-RAY DIFFRACTION6B460 - 593
10X-RAY DIFFRACTION7A594 - 716
11X-RAY DIFFRACTION8B594 - 716

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