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- PDB-2jiw: Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- ... -

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Basic information

Entry
Database: PDB / ID: 2jiw
TitleBacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- Acetylamino-2-deoxy-1-epivalienamine
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE / O-GLCNACASE / GLYCOSIDASE / EPIVALIENAMINE / GH84 / ENZYME / INHIBITOR / INHIBITION
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-BEU / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDennis, R.J. / Davies, G.J.
Citation
Journal: Org.Biomol.Chem. / Year: 2007
Title: A 1-Acetamido Derivative of 6-Epi-Valienamine: An Inhibitor of a Diverse Group of Beta-N-Acetylglucosaminidases.
Authors: Scaffidi, A. / Stubbs, K.A. / Dennis, R.J. / Taylor, E.J. / Davies, G.J. / Vocadlo, D.J. / Stick, R.V.
#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
DepositionJul 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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" AND "BB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "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)165,0714
Polymers164,6382
Non-polymers4322
Water13,799766
1
A: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5352
Polymers82,3191
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5352
Polymers82,3191
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.398, 94.131, 99.808
Angle α, β, γ (deg.)104.97, 94.09, 102.48
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116B1 - 999
2116A1 - 999

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Components

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


Mass: 82319.172 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-737
Source method: isolated from a genetically manipulated source
Details: 2-ACETYLAMINO-2-DEOXY-1-EPIVALIENAMINE
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-BEU / N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE / 2-ACETYLAMINO-2-DEOXY-1-EPIVALIENAMINE


Mass: 216.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 3.08 Å3/Da / Density % sol: 59.74 % / Description: NONE
Crystal growpH: 9 / Details: 20% PEG20K,2% DIOXANE,0.1M BICINE PH 9.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 127497 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.6 / % possible all: 94

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.95→95.35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.571 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 6220 5 %RANDOM
Rwork0.206 ---
obs0.208 117407 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.07 Å2-0.24 Å2
2--0.31 Å2-1.61 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.95→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9596 0 30 766 10392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229973
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.95313541
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43451204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03824.79499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.868151738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6711548
X-RAY DIFFRACTIONr_chiral_restr0.0950.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027706
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.24925
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.26770
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2785
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.791.56108
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30829632
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00334486
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0384.53896
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

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 4789 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.265
loose thermal1.2710
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 466
Rwork0.276 8215

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