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- PDB-5mi5: BtGH84 mutant with covalent modification by MA3 in complex with PUGNAc -

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Basic information

Entry
Database: PDB / ID: 5mi5
TitleBtGH84 mutant with covalent modification by MA3 in complex with PUGNAc
ComponentsO-GlcNAcase BT_4395
KeywordsHYDROLASE / activator
Function / homology
Function and homology information


protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / 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 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; 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
~{N}-(4-ethoxyquinazolin-2-yl)propanamide / Chem-OAN / O-GlcNAcase BT_4395
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-GlcNAcase BT_4395
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2404
Polymers83,6011
Non-polymers6393
Water4,540252
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-13 kcal/mol
Surface area30930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.221, 52.120, 112.779
Angle α, β, γ (deg.)90.00, 113.24, 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 (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4395 / Plasmid: YSBLLICPET28 / 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


Mass: 353.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N3O7
#3: Chemical ChemComp-7NQ / ~{N}-(4-ethoxyquinazolin-2-yl)propanamide


Mass: 245.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N3O2
#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.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.58 %
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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→51.815 Å / Num. obs: 58090 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.131 / Net I/σ(I): 4.3
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.588

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CHO

2cho


Resolution: 2.15→51.815 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 5498 5.01 %
Rwork0.2326 --
obs0.2345 58090 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→51.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 44 252 5781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045667
X-RAY DIFFRACTIONf_angle_d0.6347666
X-RAY DIFFRACTIONf_dihedral_angle_d4.9834787
X-RAY DIFFRACTIONf_chiral_restr0.045814
X-RAY DIFFRACTIONf_plane_restr0.005989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.17450.44291840.42923546X-RAY DIFFRACTION96
2.1745-2.20010.39682020.40563347X-RAY DIFFRACTION98
2.2001-2.22690.43851960.3743451X-RAY DIFFRACTION97
2.2269-2.25510.40421950.37663461X-RAY DIFFRACTION96
2.2551-2.28480.38631880.37213422X-RAY DIFFRACTION97
2.2848-2.31610.32641870.34843418X-RAY DIFFRACTION97
2.3161-2.34920.41331740.32273530X-RAY DIFFRACTION97
2.3492-2.38420.37512070.32443468X-RAY DIFFRACTION96
2.3842-2.42150.32071760.32093365X-RAY DIFFRACTION97
2.4215-2.46120.36941710.31133388X-RAY DIFFRACTION95
2.4612-2.50360.34261550.30133447X-RAY DIFFRACTION95
2.5036-2.54910.3681950.2863411X-RAY DIFFRACTION97
2.5491-2.59820.28811730.26873489X-RAY DIFFRACTION97
2.5982-2.65120.35121970.26413448X-RAY DIFFRACTION98
2.6512-2.70880.33161680.25623525X-RAY DIFFRACTION98
2.7088-2.77190.26981810.25663502X-RAY DIFFRACTION97
2.7719-2.84120.23351700.22843521X-RAY DIFFRACTION98
2.8412-2.9180.30741640.23073517X-RAY DIFFRACTION97
2.918-3.00380.26022090.23563473X-RAY DIFFRACTION98
3.0038-3.10080.29341820.2283480X-RAY DIFFRACTION97
3.1008-3.21160.26162060.22093388X-RAY DIFFRACTION96
3.2116-3.34020.25412020.23463479X-RAY DIFFRACTION97
3.3402-3.49210.26411640.23043554X-RAY DIFFRACTION99
3.4921-3.67620.25061560.19613534X-RAY DIFFRACTION99
3.6762-3.90650.20031850.18413533X-RAY DIFFRACTION99
3.9065-4.2080.20831970.18923519X-RAY DIFFRACTION99
4.208-4.63120.21711910.17033457X-RAY DIFFRACTION97
4.6312-5.30080.24521730.17173512X-RAY DIFFRACTION98
5.3008-6.67610.24191860.20473556X-RAY DIFFRACTION99
6.6761-51.82990.20311640.18153521X-RAY DIFFRACTION98
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)
10.9894-0.1185-0.00792.0160.24572.11690.1301-0.2156-0.11980.3139-0.09940.00850.1047-0.3101-0.05540.5379-0.0362-0.12260.33540.0410.275715.2049-4.399247.7601
20.91620.33580.14921.40150.30020.97240.00780.0376-0.0516-0.02860.0093-0.2537-0.03990.1234-0.01240.18150.00860.01840.2449-0.00360.249930.05488.629322.4968
30.97120.3770.26541.21430.32451.30140.16310.0516-0.1693-0.18950.0013-0.07510.4770.035-0.15050.4210.0639-0.08650.23720.00350.258511.9649-17.26975.254
40.35730.05060.0611.6596-0.30170.663-0.02240.13380.0487-0.50440.0491-0.30460.07520.12520.00340.36410.05830.06310.3375-0.02030.303715.666-8.3589-12.3214
50.8817-0.1590.06560.60410.22810.10670.04990.16770.0291-0.6949-0.1634-0.64-0.09020.4674-0.0920.76150.01610.37610.90810.10860.860227.15099.1265-24.5512
62.3972-1.15550.53573.9643-0.22462.0312-0.06-0.2271-0.1-0.00230.0777-0.28540.05970.29270.03210.3337-0.01850.24060.57250.00910.703321.27138.1767-15.0743
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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