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- PDB-5fky: Structure of a hydrolase bound with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 5fky
TitleStructure of a hydrolase bound with an inhibitor
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE
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-2J4 / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsCekic, N. / Heinonen, J.E. / Stubbs, K.A. / Roth, C. / McEachern, E.J. / Davies, G.J. / Vocadlo, D.J.
CitationJournal: Chem Sci / Year: 2016
Title: Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by humanO-GlcNAcase.
Authors: Cekic, N. / Heinonen, J.E. / Stubbs, K.A. / Roth, C. / He, Y. / Bennet, A.J. / McEachern, E.J. / Davies, G.J. / Vocadlo, D.J.
History
DepositionOct 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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. SHEET DETERMINATION METHOD: DSSP 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)165,1655
Polymers164,6322
Non-polymers5333
Water16,304905
1
A: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6283
Polymers82,3161
Non-polymers3122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5362
Polymers82,3161
Non-polymers2201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.440, 93.690, 99.020
Angle α, β, γ (deg.)104.07, 94.18, 102.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein O-GLCNACASE BT_4395 / BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B ...BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B / N-ACETYL-BETA-GLUCOSAMINIDASE / GLYCOSIDE HYDROLASE


Mass: 82316.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, protein O-GlcNAcase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-2J4 / (3aR,5R,6S,7R,7aR)-2-amino-5-(hydroxymethyl)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol


Mass: 220.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / 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: 2.71 Å3/Da / Density % sol: 54.8 % / Description: NONE

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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: 1.8→33.8 Å / Num. obs: 153821 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.8→95.17 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.92 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24855 7706 5 %RANDOM
Rwork0.21112 ---
obs0.21299 146115 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.748 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0.12 Å2-0.35 Å2
2--0.31 Å2-0.64 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→95.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10466 0 34 905 11405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910839
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210248
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.95514695
X-RAY DIFFRACTIONr_angle_other_deg1.012323643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5851299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24724.822535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.523151893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.671552
X-RAY DIFFRACTIONr_chiral_restr0.1030.21568
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022517
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_it0.2560.5385166
X-RAY DIFFRACTIONr_mcbond_other0.2560.5385165
X-RAY DIFFRACTIONr_mcangle_it0.4640.8056442
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3010.5625673
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 553 -
Rwork0.389 10499 -
obs--93.05 %
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)
13.74791.1147-0.17913.28830.8462.69630.00460.17510.7355-0.2798-0.02330.3151-0.7899-0.22190.01880.30980.06850.01280.2249-0.09810.3314-4.53426.6556.215
21.77820.17610.52670.83250.26471.34440.0443-0.2089-0.0490.0849-0.0611-0.05020.102-0.13480.01680.0201-0.0390.01330.1271-0.05560.04415.516-3.0974.761
32.00660.71670.79162.01630.52191.78330.0413-0.0215-0.1023-0.0665-0.09690.22790.1806-0.31440.05560.072-0.05080.01130.2353-0.10070.0837-14.878-14.815-21.79
44.1315-1.68980.79410.7879-0.27090.2528-0.063-0.4464-0.79350.17530.20080.13260.2423-0.0215-0.13780.6920.02420.03950.67930.04150.76243.328-33.514-19.806
52.8474-0.83970.27274.01960.67051.9641-0.0417-0.2415-0.46120.37460.04290.08310.498-0.1033-0.00130.1823-0.0364-0.00220.179-0.06180.1607-11.163-69.87731.469
61.54140.1313-0.21760.80240.11211.2849-0.01330.12290.0254-0.05960.0012-0.0622-0.0703-0.02670.0120.01130.0181-0.00950.099-0.060.0502-2.067-39.91932.051
72.1408-0.5827-0.50061.88560.45041.5986-0.0055-0.09840.19310.0551-0.08080.2466-0.1615-0.24980.08640.06710.0258-0.01810.2046-0.10690.11-21.923-27.58258.705
84.89722.3011-0.77312.41390.43581.2475-0.02830.5270.8782-0.29650.08570.0212-0.5518-0.0143-0.05740.40980.0064-0.06690.44660.07390.5745-2.135-9.00156.055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 124
2X-RAY DIFFRACTION2A125 - 457
3X-RAY DIFFRACTION3A458 - 582
4X-RAY DIFFRACTION4A583 - 715
5X-RAY DIFFRACTION5B4 - 128
6X-RAY DIFFRACTION6B129 - 459
7X-RAY DIFFRACTION7B460 - 588
8X-RAY DIFFRACTION8B589 - 715

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