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- PDB-2j4g: Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with n-b... -

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Basic information

Entry
Database: PDB / ID: 2j4g
TitleBacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with n-butyl- thiazoline inhibitor
ComponentsHYALURONOGLUCOSAMINIDASE
KeywordsINHIBITOR / GH84 / ENZYME / THIAZOLINE / INHIBITION / O-GLCNACASE
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 / 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 / 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
ACETATE ION / Chem-NB1 / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDennis, R.J. / Davies, G.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2007
Title: Analysis of Pugnac and Nag-Thiazoline as Transition State Analogues for Human O-Glcnacase: Mechanistic and Structural Insights Into Inhibitor Selectivity and Transition State Poise.
Authors: Whitworth, G.E. / Macauley, M.S. / Stubbs, K.A. / Dennis, R.J. / Taylor, E.J. / Davies, G.J. / Greig, I.R. / Vocadlo, D.J.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure and Mechanism of a Bacterial Beta-Glucosaminidase Having O-Glcnacase Activity
Authors: Dennis, R.J. / Taylor, E.J. / Macauley, M.S. / Stubbs, K.A. / Turkenburg, J.P. / Hart, S.J. / Black, G.N. / Vocadlo, D.J. / Davies, G.J.
History
DepositionAug 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

Deposited unit
A: HYALURONOGLUCOSAMINIDASE
B: HYALURONOGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1738
Polymers164,3762
Non-polymers7976
Water10,052558
1
A: HYALURONOGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5864
Polymers82,1881
Non-polymers3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYALURONOGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5864
Polymers82,1881
Non-polymers3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)185.106, 51.711, 172.782
Angle α, β, γ (deg.)90.00, 100.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2250-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 999
2112B1 - 999
1121A1590
2121B1590

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.99928, -0.00063, -0.03781), (0.00066, 1, 0.00077), (0.03781, -0.00079, 0.99928)
Vector: -15.43601, -0.35141, 85.03981)

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Components

#1: Protein HYALURONOGLUCOSAMINIDASE / O-GLCNACASE


Mass: 82187.984 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-737
Source method: isolated from a genetically manipulated source
Details: N-BUTYL-THIAZOLINE
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89ZI2, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-NB1 / (3AR,5R,6S,7R,7AR)-5-(HYDROXYMETHYL)-2-PROPYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL


Mass: 247.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO4S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSIGNAL PEPTIDE FROM RESIDUE 1-22. SEQUENCE CLONED FROM N23. NUMBERED IN PDB AS IN MATURE PROTEIN, ...SIGNAL PEPTIDE FROM RESIDUE 1-22. SEQUENCE CLONED FROM N23. NUMBERED IN PDB AS IN MATURE PROTEIN, GLN1, ASN2, ETC.

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 6
Details: 0.4M SODIUM ACETATE,13%(V/V)PEG 3500, 0.1M MES PH6.0, 10% (V/V) GLYCEROL, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 77267 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHO

2cho


Resolution: 2.25→169.03 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.002 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3870 5 %RANDOM
Rwork0.22 ---
obs0.223 73055 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-1.79 Å2
2---1.17 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.25→169.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9457 0 52 558 10067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.95413241
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.99551163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66724.847489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.627151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0211547
X-RAY DIFFRACTIONr_chiral_restr0.1180.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027517
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.24665
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26617
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2591
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7881.56005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34529427
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93234371
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8824.53805
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2319tight positional0.060.05
21A16tight positional0.030.05
22B16tight positional0.030.05
11A2379medium positional0.350.5
11A2319tight thermal0.130.5
21A16tight thermal0.240.5
22B16tight thermal0.240.5
11A2379medium thermal0.692
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.42 341
Rwork0.338 5132

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