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- PDB-5onz: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

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Basic information

Entry
Database: PDB / ID: 5onz
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with glucosylglycolate
ComponentsHydrolase
KeywordsHYDROLASE / Mycobacterium
Function / homology
Function and homology information


glucosylglycerate hydrolase / glucosylglycerate hydrolase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process
Similarity search - Function
Glycoside hydrolase family 63 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
(alpha-D-glucopyranosyloxy)acetic acid / SERINE / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCereija, T.B. / Macedo-Ribeiro, S. / Pereira, P.J.B.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 Portugal
Norte Portugal Regional Operational Programme NORTE 2020Norte-01-0145-FEDER-000012 Portugal
CitationJournal: Iucrj / Year: 2019
Title: The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation.
Authors: Cereija, T.B. / Alarico, S. / Lourenco, E.C. / Manso, J.A. / Ventura, M.R. / Empadinhas, N. / Macedo-Ribeiro, S. / Pereira, P.J.B.
History
DepositionAug 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,13322
Polymers101,8272
Non-polymers2,30620
Water12,196677
1
A: Hydrolase
B: Hydrolase
hetero molecules

A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,26644
Polymers203,6544
Non-polymers4,61240
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area14900 Å2
ΔGint-28 kcal/mol
Surface area59260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.223, 158.901, 87.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hydrolase /


Mass: 50913.484 Da / Num. of mol.: 2 / Mutation: D182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Gene: C731_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDL0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-9YW / (alpha-D-glucopyranosyloxy)acetic acid / Glucosylglycolate / (alpha-D-glucosyloxy)acetic acid / (D-glucosyloxy)acetic acid / (glucosyloxy)acetic acid


Type: D-saccharide / Mass: 238.192 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H14O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris-Bicine pH 8.5, amino acids, PEG 4000, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.93→48.67 Å / Num. obs: 91224 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.056 / Rrim(I) all: 0.139 / Net I/σ(I): 8.8
Reflection shellResolution: 1.93→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.227 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.56 / Rpim(I) all: 0.533 / Rrim(I) all: 1.34 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHZ

5ohz


Resolution: 1.93→48.668 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.08
RfactorNum. reflection% reflection
Rfree0.1846 4566 5.01 %
Rwork0.1491 --
obs0.1509 91157 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→48.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 152 677 7989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017837
X-RAY DIFFRACTIONf_angle_d0.98410690
X-RAY DIFFRACTIONf_dihedral_angle_d20.0484617
X-RAY DIFFRACTIONf_chiral_restr0.0591097
X-RAY DIFFRACTIONf_plane_restr0.0071404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9305-1.95240.30771340.26652773X-RAY DIFFRACTION96
1.9524-1.97540.30421610.26442824X-RAY DIFFRACTION100
1.9754-1.99950.27441500.2492883X-RAY DIFFRACTION100
1.9995-2.02480.25151470.22652826X-RAY DIFFRACTION100
2.0248-2.05140.25781580.22432900X-RAY DIFFRACTION100
2.0514-2.07950.24711760.21522781X-RAY DIFFRACTION100
2.0795-2.10920.2481500.20562876X-RAY DIFFRACTION100
2.1092-2.14070.24191440.19432864X-RAY DIFFRACTION100
2.1407-2.17420.22041460.18592854X-RAY DIFFRACTION100
2.1742-2.20980.21381590.16732875X-RAY DIFFRACTION100
2.2098-2.24790.19491560.15972835X-RAY DIFFRACTION100
2.2479-2.28880.22191310.1642895X-RAY DIFFRACTION100
2.2888-2.33280.22781340.15752906X-RAY DIFFRACTION100
2.3328-2.38040.17841430.15522868X-RAY DIFFRACTION100
2.3804-2.43220.20631600.15372844X-RAY DIFFRACTION100
2.4322-2.48880.21481630.15062871X-RAY DIFFRACTION100
2.4888-2.5510.18181570.15242873X-RAY DIFFRACTION99
2.551-2.620.1981410.15172891X-RAY DIFFRACTION100
2.62-2.6970.1851560.1422873X-RAY DIFFRACTION100
2.697-2.78410.16661540.13922893X-RAY DIFFRACTION100
2.7841-2.88360.17681360.13982891X-RAY DIFFRACTION100
2.8836-2.9990.15271690.13652887X-RAY DIFFRACTION100
2.999-3.13550.18911400.13282900X-RAY DIFFRACTION100
3.1355-3.30080.18591440.13572934X-RAY DIFFRACTION100
3.3008-3.50750.16941360.13312906X-RAY DIFFRACTION100
3.5075-3.77820.14961550.11982917X-RAY DIFFRACTION100
3.7782-4.15830.15411730.11462916X-RAY DIFFRACTION100
4.1583-4.75950.14751750.11342940X-RAY DIFFRACTION100
4.7595-5.99480.17271630.14852969X-RAY DIFFRACTION100
5.9948-48.68320.17961550.16633126X-RAY DIFFRACTION99
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)
11.23090.67850.25934.9292-1.16624.1838-0.04020.067-0.0962-0.34740.08310.12270.1096-0.1649-0.02710.1520.0119-0.01310.1126-0.02190.175442.29338.874937.5205
23.6469-1.45082.23242.1016-1.34284.98940.17450.367-0.0191-0.5427-0.09950.029-0.0350.0516-0.09750.32-0.00190.0230.1514-0.01060.183546.547221.310628.2588
30.99380.09850.01221.2841-0.05871.1153-0.01460.05150.1651-0.13580.0140.1782-0.2185-0.0902-0.00720.21890.0254-0.01340.13850.00950.216739.455127.637441.9477
41.94551.42741.52862.23591.3793.94910.2681-0.4413-0.06640.5549-0.2615-0.0880.10410.1148-0.01060.3097-0.1180.00520.34660.03710.18352.575611.869886.8854
51.47280.25810.06291.3368-0.05411.46150.1575-0.36120.10510.3334-0.1811-0.195-0.25210.22870.04770.3325-0.1237-0.03340.3168-0.01830.205360.871324.971881.5476
61.0849-0.02650.10862.429-0.74782.02880.0581-0.018-0.1284-0.0362-0.1089-0.28680.01790.25880.03610.1335-0.024-0.00620.1978-0.00320.20662.947911.906767.0201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 446 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 117 )
5X-RAY DIFFRACTION5chain 'B' and (resid 118 through 320 )
6X-RAY DIFFRACTION6chain 'B' and (resid 321 through 446 )

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