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- PDB-2wzi: BtGH84 D243N in complex with 5F-oxazoline -

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Basic information

Entry
Database: PDB / ID: 2wzi
TitleBtGH84 D243N in complex with 5F-oxazoline
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-5FN / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionNov 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)170,20313
Polymers169,1742
Non-polymers1,02911
Water20,1411118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-45.5 kcal/mol
Surface area52890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.380, 93.820, 98.880
Angle α, β, γ (deg.)104.14, 94.06, 103.08
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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: 84586.938 Da / Num. of mol.: 2 / Mutation: YES
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

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Non-polymers , 5 types, 1129 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-5FN / (3AS,5S,6S,7R,7AR)-5-FLUORO-5-(HYDROXYMETHYL)-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]OXAZOLE-6,7-DIOL


Mass: 221.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12FNO5
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 264 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 264 TO ASN

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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: 2.79 Å3/Da / Density % sol: 55.92 % / Description: NONE
Crystal growDetails: 0.6M NH4AC, 10% GLYCEROL, 14% PEG3350, 0.1M MES PH6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→34.33 Å / Num. obs: 132087 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 94.9

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Processing

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

2cho


Resolution: 1.9→34.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.784 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22349 6621 5 %RANDOM
Rwork0.18409 ---
obs0.18608 124524 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.829 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0.42 Å2-0.5 Å2
2--0.59 Å2-1.75 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10361 0 64 1118 11543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.95914736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93251297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3224.888536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.549151885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4761551
X-RAY DIFFRACTIONr_chiral_restr0.0920.21564
X-RAY DIFFRACTIONr_gen_planes_refined
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_it0.5631.56489
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.949210523
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.79834375
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7074.54210
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 490 -
Rwork0.293 9032 -
obs--95.08 %
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)
12.6128-0.73510.34885.11591.39412.5093-0.0058-0.0811-0.39720.36390.00420.10160.5233-0.11740.00150.1935-0.0379-0.00640.07590.010.1209-25.5834-33.2167-3.322
21.79520.1721-0.32250.9310.21851.4144-0.01230.09570.0427-0.05990.0155-0.0464-0.0631-0.0109-0.00320.06650.0104-0.01870.01640.00980.0268-16.7122-4.1162-1.6982
32.3318-0.8581-0.70312.38860.87581.97210.0077-0.14570.28470.1103-0.13690.1605-0.1583-0.26780.12930.12530.0271-0.03730.13-0.04620.1011-35.5288.219324.813
42.97151.4043-0.27375.06651.41483.21420.0635-0.14280.7851-0.3391-0.2070.3829-0.7483-0.44080.14350.260.10210.02910.1743-0.11330.3251-26.153534.107767.8142
52.06890.25590.73570.93820.3681.57240.0558-0.1905-0.05180.0732-0.0734-0.06420.1142-0.14250.01760.0646-0.01220.02090.02710.01110.0256-16.15425.667965.3989
62.5651.12570.89112.43871.13632.060.05720.019-0.2115-0.0718-0.14780.12450.1633-0.23330.09060.1217-0.02660.03080.1614-0.03320.0604-35.2887-6.55538.9195
78.74892.38631.26444.93510.63763.1872-0.16180.66781.3253-0.34040.11110.0157-0.31870.12830.05070.38280.0094-0.04870.26820.20050.6365-15.256326.875521.2435
811.7318-3.5084-1.41835.73941.50714.9416-0.3041-0.7637-1.49490.52080.29590.18810.60820.28670.00820.38430.0250.0150.31970.17080.6049-15.3175-25.002342.3356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 128
2X-RAY DIFFRACTION2A129 - 459
3X-RAY DIFFRACTION2A1719
4X-RAY DIFFRACTION3A460 - 593
5X-RAY DIFFRACTION4B2 - 128
6X-RAY DIFFRACTION5B129 - 459
7X-RAY DIFFRACTION5B1721
8X-RAY DIFFRACTION6B460 - 593
9X-RAY DIFFRACTION7A594 - 716
10X-RAY DIFFRACTION8B594 - 716

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