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- PDB-5mi7: BtGH84 mutant with covalent modification by MA4 in complex with PUGNAc -

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Basic information

Entry
Database: PDB / ID: 5mi7
TitleBtGH84 mutant with covalent modification by MA4 in complex with PUGNAc
ComponentsO-GlcNAcase BT_4395
KeywordsHYDROLASE / activator
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-7NT / Chem-OAN / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDarby, J.F. / Davies, G.J. / Hubbard, R.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N008332/1 United Kingdom
CitationJournal: Chem Sci / Year: 2017
Title: Increase of enzyme activity through specific covalent modification with fragments.
Authors: Darby, J.F. / Atobe, M. / Firth, J.D. / Bond, P. / Davies, G.J. / O'Brien, P. / Hubbard, R.E.
History
DepositionNov 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-GlcNAcase BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2874
Polymers83,6011
Non-polymers6863
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-14 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.193, 51.823, 108.234
Angle α, β, γ (deg.)90.00, 111.61, 90.00
Int Tables number5
Space group name H-MC121

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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


Mass: 83601.453 Da / Num. of mol.: 1 / Mutation: C420S, Y550C, C654S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4395 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q89ZI2, protein O-GlcNAcase, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-OAN / O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE / PUGNAc / PUGNAc


Mass: 353.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N3O7 / Comment: inhibitor*YM
#3: Chemical ChemComp-7NT / ~{N}-(4-morpholin-4-ylthieno[2,3-d]pyrimidin-2-yl)propanamide


Mass: 292.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N4O2S
#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 / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4% PEG 8K, 125mM Imidazole, 3% TMAO, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→100.62 Å / Num. obs: 59272 / % possible obs: 100 % / Redundancy: 4 % / CC1/2: 0.996 / Net I/σ(I): 6.9
Reflection shellResolution: 2.1→2.16 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CHO

2cho


Resolution: 2.1→100.62 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.32
RfactorNum. reflection% reflection
Rfree0.2488 5637 5.02 %
Rwork0.2126 --
obs0.2143 58982 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→100.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5447 0 46 141 5634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045636
X-RAY DIFFRACTIONf_angle_d0.5817620
X-RAY DIFFRACTIONf_dihedral_angle_d12.3583384
X-RAY DIFFRACTIONf_chiral_restr0.043807
X-RAY DIFFRACTIONf_plane_restr0.004984
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)
12.9376-0.2896-0.62823.55890.50195.0570.0597-0.3685-0.1950.5748-0.00230.13220.1176-0.3815-0.0440.3699-0.0165-0.05510.32850.07830.273916.797-4.462446.7206
20.93390.19650.1382.15250.00061.67790.06240.0981-0.1217-0.1177-0.0057-0.3446-0.05930.2713-0.03930.18330.019-0.02660.2398-0.02520.265430.41728.63321.2089
30.84450.6979-0.08891.89861.28531.63150.06660.083-0.2586-0.32260.0269-0.01060.53320.1739-0.05360.6160.119-0.17770.2855-0.02410.396512.1435-17.13784.7135
40.4656-0.2772-0.30323.20560.28071.31410.02970.18410.0167-0.4580.1755-0.39470.2260.1588-0.20250.53820.0682-0.07630.3754-0.05450.381314.7053-8.4427-12.4601
51.4088-0.45-1.40931.271-0.0051.59330.06620.648-0.0614-0.45770.2175-0.6864-0.14431.0582-0.2840.70040.04420.31730.8551-0.14830.515525.44859.4764-25.0641
65.1093-5.20933.70158.4801-1.81238.6542-0.2253-0.6189-0.44280.53150.2349-0.07870.21540.67980.02470.31890.02880.06960.5009-0.04840.604920.61597.7956-15.6845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:128)
2X-RAY DIFFRACTION2(chain A and resid 129:407)
3X-RAY DIFFRACTION3(chain A and resid 408:523)
4X-RAY DIFFRACTION4(chain A and resid 524:645)
5X-RAY DIFFRACTION5(chain A and resid 646:707)
6X-RAY DIFFRACTION6(chain A and resid 708:715)

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