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- PDB-2xj7: BtGH84 in complex with 6-acetamido-6-deoxy-castanospermine -

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Basic information

Entry
Database: PDB / ID: 2xj7
TitleBtGH84 in complex with 6-acetamido-6-deoxy-castanospermine
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE / INHIBITOR
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
6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHe, Y. / Davies, G.J.
CitationJournal: Chem.Biol. / Year: 2010
Title: Inhibition of O-Glcnacase Using a Potent and Cell-Permeable Inhibitor Does not Induce Insulin Resistance in 3T3-L1 Adipocytes.
Authors: Macauley, M.S. / He, Y. / Gloster, T.M. / Stubbs, K.A. / Davies, G.J. / Vocadlo, D.J.
History
DepositionJul 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / 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. 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)165,1736
Polymers164,6322
Non-polymers5414
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-23.5 kcal/mol
Surface area53210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.493, 93.981, 98.815
Angle α, β, γ (deg.)104.13, 93.88, 103.13
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 82316.109 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: Chemical ChemComp-GC2 / 6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE / N-[(1S,6S,7R,8R,8AR)-1,7,8-TRIHYDROXYOCTAHYDROINDOLIZIN-6-YL]ACETAMIDE


Mass: 230.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 0.3M NH4AC, 0.1M MES PH6.0, 13% PEG3350(W/V),10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9802
DetectorType: ADSC CCD / Detector: CCD / Date: May 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 114491 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / % possible all: 96.8

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Processing

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

2cho


Resolution: 2→47.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.705 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23914 5654 4.9 %RANDOM
Rwork0.20288 ---
obs0.2047 108834 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.289 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å2-1.08 Å2-1.16 Å2
2--0.61 Å2-3.42 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10310 0 34 392 10736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.95814541
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50751280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87424.886526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.281151869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1581550
X-RAY DIFFRACTIONr_chiral_restr0.1070.21553
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218193
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_it0.8061.56426
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.289210408
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32534300
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3554.54129
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: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 419 -
Rwork0.307 7883 -
obs--95.1 %
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)
12.85-0.46790.71884.13471.30613.2219-0.0234-0.094-0.51460.3764-0.08630.08810.5939-0.25930.10970.2984-0.05450.02270.05810.04920.187-8.9158-69.075732.5534
21.43580.3445-0.05740.96420.50471.6092-0.03620.19890.0036-0.0813-0.0052-0.0458-0.1003-0.07630.04140.11980.0231-0.01050.06140.04210.081-0.1159-39.321733.486
32.2419-0.7496-0.65161.96370.77541.74480.035-0.1510.26640.0401-0.17770.205-0.1842-0.26820.14260.17610.0452-0.03940.168-0.02840.1385-18.9367-26.818759.993
48.0223-0.3018-1.28383.02350.31133.9012-0.06240.54111.0673-0.24640.0032-0.0796-0.48940.1250.05920.4991-0.0266-0.05870.30650.11720.63631.5336-8.375957.031
52.67821.3692-0.233.98181.08582.8375-0.03560.01330.6928-0.3536-0.06570.3432-0.7031-0.280.10140.33370.08010.00820.1508-0.02620.3335-9.22650.3768102.377
61.82450.21760.7240.93710.68351.86760.0851-0.1668-0.09080.0994-0.0818-0.03910.1359-0.152-0.00330.1043-0.01370.02340.04790.05040.08130.3084-29.1007100.7651
72.38291.10251.09172.08830.89992.36220.1020.1369-0.2513-0.0553-0.19030.15250.2312-0.29910.08830.1595-0.02020.03860.1935-0.03430.1293-18.8682-41.524274.4455
811.0672-0.73090.38247.5056-0.17651.3545-0.174-0.6707-1.3650.27070.219-0.10.47950.2934-0.0450.52620.02750.01410.50820.03750.59481.2393-59.73976.6745
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 DIFFRACTION4A594 - 716
6X-RAY DIFFRACTION5B4 - 128
7X-RAY DIFFRACTION6B129 - 459
8X-RAY DIFFRACTION6B1000
9X-RAY DIFFRACTION7B460 - 593
10X-RAY DIFFRACTION8B594 - 716

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