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- PDB-5abg: Structure of GH84 with ligand -

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Basic information

Entry
Database: PDB / ID: 5abg
TitleStructure of GH84 with ligand
ComponentsO-GLCNACASE BT_4395
KeywordsHYDROLASE / GH84 GLYCOSIDE HYDROLASE / TIM-BARREL / 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
Chem-V0N / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsBergeron-Brlek, M. / Goodwin-Tindall, J. / Cekic, N. / Varghese, V. / Zandberg, W.F. / Shan, X. / Roth, C. / Chan, S. / Davies, G.J. / Vocadlo, D.J. / Britton, R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.
Authors: Bergeron-Brlek, M. / Goodwin-Tindall, J. / Cekic, N. / Roth, C. / Zandberg, W.F. / Shan, X. / Varghese, V. / Chan, S. / Davies, G.J. / Vocadlo, D.J. / Britton, R.
History
DepositionAug 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Structure summary
Revision 1.2Jan 27, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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)167,8607
Polymers167,0152
Non-polymers8455
Water5,260292
1
A: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9103
Polymers83,5071
Non-polymers4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-GLCNACASE BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9504
Polymers83,5071
Non-polymers4433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.531, 161.184, 223.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 83507.398 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: Q89ZI2, protein O-GlcNAcase, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-V0N / 2-[(2R,3S,4R,5R)-1-[3-(4-fluorophenyl)propyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidin-2-yl]-N-methyl-ethanamide


Mass: 340.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25FN2O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.9 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→49.08 Å / Num. obs: 126740 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 35.63 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→48.442 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 12009 5 %
Rwork0.2045 --
obs0.2061 126463 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.69 Å2
Refinement stepCycle: LAST / Resolution: 2→48.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10759 0 57 292 11108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311098
X-RAY DIFFRACTIONf_angle_d0.77615023
X-RAY DIFFRACTIONf_dihedral_angle_d13.4564193
X-RAY DIFFRACTIONf_chiral_restr0.0311600
X-RAY DIFFRACTIONf_plane_restr0.0031939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.44533930.37947559X-RAY DIFFRACTION99
2.0227-2.04650.40064380.3677711X-RAY DIFFRACTION99
2.0465-2.07150.41954170.35847660X-RAY DIFFRACTION99
2.0715-2.09770.33394130.34817521X-RAY DIFFRACTION99
2.0977-2.12530.31933540.32067817X-RAY DIFFRACTION99
2.1253-2.15440.3643880.30937654X-RAY DIFFRACTION99
2.1544-2.18520.29873720.29617621X-RAY DIFFRACTION99
2.1852-2.21780.29633990.28857688X-RAY DIFFRACTION99
2.2178-2.25250.34813630.28277730X-RAY DIFFRACTION99
2.2525-2.28940.28353890.26727549X-RAY DIFFRACTION99
2.2894-2.32890.29174040.25527714X-RAY DIFFRACTION99
2.3289-2.37120.29054210.24517636X-RAY DIFFRACTION99
2.3712-2.41680.30474030.24387630X-RAY DIFFRACTION99
2.4168-2.46620.31023990.25097689X-RAY DIFFRACTION99
2.4662-2.51980.23463970.22217640X-RAY DIFFRACTION100
2.5198-2.57840.24613560.21197736X-RAY DIFFRACTION99
2.5784-2.64290.27663590.21147628X-RAY DIFFRACTION99
2.6429-2.71430.21873590.21237760X-RAY DIFFRACTION99
2.7143-2.79420.27993650.20197595X-RAY DIFFRACTION99
2.7942-2.88440.24214330.19777641X-RAY DIFFRACTION99
2.8844-2.98740.25774330.1997592X-RAY DIFFRACTION99
2.9874-3.1070.25664030.21827586X-RAY DIFFRACTION99
3.107-3.24840.27344100.21347658X-RAY DIFFRACTION99
3.2484-3.41960.22974180.19987519X-RAY DIFFRACTION98
3.4196-3.63380.23054420.19017529X-RAY DIFFRACTION98
3.6338-3.91430.20433900.17747531X-RAY DIFFRACTION98
3.9143-4.3080.18674380.16367464X-RAY DIFFRACTION97
4.308-4.93080.15943980.14667466X-RAY DIFFRACTION98
4.9308-6.21020.20294510.16437483X-RAY DIFFRACTION97
6.2102-48.45580.19114040.17127419X-RAY DIFFRACTION96
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)
11.90431.45990.0795.18330.65561.9129-0.3420.6083-0.5302-0.60230.45870.39160.6641-0.4971-0.07740.8244-0.2948-0.06150.8774-0.00790.48516.654722.4844223.1711
21.5510.76790.5092.64640.50442.5874-0.33890.9427-0.3322-0.80070.47530.18070.4079-0.6564-0.05980.6823-0.2793-0.01070.9779-0.04050.506519.382228.4091223.2608
32.08590.3852-0.50471.3413-0.51391.777-0.01940.32150.20140.00770.1420.0498-0.0983-0.1925-0.13750.35980.0167-0.00530.46560.08670.345130.762146.9485239.2231
41.71160.0671-0.83640.44790.73482.20460.0291-0.01460.06170.0767-0.06190.17560.0083-0.79970.08010.40920.01620.00050.74510.14050.39346.014736.5138264.3781
56.27190.0226-1.39750.43550.25180.4532-0.0014-0.74910.57340.17030.0948-0.0116-0.232-0.3045-0.10170.53340.10040.00120.68450.04560.43111.916946.6382274.9702
62.24471.35112.6631.0182.0515.7839-0.4795-0.13280.3352-0.3184-0.1206-0.2359-1.3861-0.66130.51590.93940.2051-0.18140.64550.02440.695629.997453.6829283.5515
71.7239-0.2073-0.56222.10551.73574.21820.033-0.38470.35070.06390.00060.0263-0.38180.011-0.01990.3927-0.02-0.00380.4111-0.08120.389118.082226.7935316.6362
83.66920.3941-0.19741.38850.07162.0768-0.09-0.0603-0.37430.00690.0403-0.32820.22930.21030.04710.3465-0.03460.02260.2533-0.030.401839.99829.0151302.0122
91.90870.1578-0.05121.0422-0.65732.2832-0.1457-0.0254-0.7281-0.05930.091-0.20240.498-0.2595-0.01940.5264-0.07930.02760.2407-0.02030.618225.4891-4.0747301.2278
101.0843-0.20570.50760.6851-0.20082.3065-0.03060.3315-0.0843-0.25730.13940.12680.2603-0.4821-0.09010.4643-0.1736-0.02120.5640.02820.39069.288313.4451278.6286
113.5055-0.9514-0.23018.7794-1.72586.79490.08780.43510.0581-0.7941-0.1121-1.06490.38490.72030.04860.9121-0.02110.08110.9994-0.11970.684429.7791-1.0132255.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 44 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 45 THROUGH 142 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 143 THROUGH 410 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 411 THROUGH 544 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 545 THROUGH 616 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 617 THROUGH 715 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 2 THROUGH 142 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 143 THROUGH 278 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 279 THROUGH 348 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 349 THROUGH 616 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 617 THROUGH 715 )

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