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

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Basic information

Entry
Database: PDB / ID: 5ohc
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) in complex with glycerol
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
Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJul 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 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.identifier_ORCID / _citation_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)102,83612
Polymers101,9152
Non-polymers92110
Water12,701705
1
A: Hydrolase
B: Hydrolase
hetero molecules

A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,67224
Polymers203,8304
Non-polymers1,84220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)85.853, 159.282, 91.221
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: 50957.496 Da / Num. of mol.: 2
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.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→40.28 Å / Num. obs: 84736 / % possible obs: 99.6 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.042 / Rrim(I) all: 0.094 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.04 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.276 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.559 / Rpim(I) all: 0.622 / Rrim(I) all: 1.426 / % possible all: 99.8

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Processing

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

5ohz


Resolution: 2→40.279 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.27
RfactorNum. reflection% reflection
Rfree0.2098 4330 5.11 %
Rwork0.1668 --
obs0.1689 84685 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→40.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7166 0 60 705 7931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017637
X-RAY DIFFRACTIONf_angle_d0.99310419
X-RAY DIFFRACTIONf_dihedral_angle_d17.3714492
X-RAY DIFFRACTIONf_chiral_restr0.0571068
X-RAY DIFFRACTIONf_plane_restr0.0071371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.3451480.32812649X-RAY DIFFRACTION100
2.0227-2.04650.40411290.31722678X-RAY DIFFRACTION100
2.0465-2.07150.3731430.30342645X-RAY DIFFRACTION100
2.0715-2.09770.34911320.27642630X-RAY DIFFRACTION100
2.0977-2.12530.31921490.2672678X-RAY DIFFRACTION100
2.1253-2.15440.29421550.24892647X-RAY DIFFRACTION100
2.1544-2.18520.2881280.23992668X-RAY DIFFRACTION100
2.1852-2.21780.28231560.22152622X-RAY DIFFRACTION100
2.2178-2.25250.2691590.22792650X-RAY DIFFRACTION100
2.2525-2.28940.26981700.21442647X-RAY DIFFRACTION100
2.2894-2.32890.26611230.20192688X-RAY DIFFRACTION100
2.3289-2.37120.23761330.1952679X-RAY DIFFRACTION100
2.3712-2.41680.2511360.19282649X-RAY DIFFRACTION99
2.4168-2.46610.23661520.18592672X-RAY DIFFRACTION100
2.4661-2.51970.23691430.17492653X-RAY DIFFRACTION100
2.5197-2.57840.22791540.17622640X-RAY DIFFRACTION99
2.5784-2.64280.2021490.17192635X-RAY DIFFRACTION99
2.6428-2.71430.2181260.1662671X-RAY DIFFRACTION99
2.7143-2.79410.2171550.17172636X-RAY DIFFRACTION98
2.7941-2.88430.22241360.16552647X-RAY DIFFRACTION98
2.8843-2.98730.211580.16042643X-RAY DIFFRACTION99
2.9873-3.10690.1981780.15812635X-RAY DIFFRACTION99
3.1069-3.24820.20921490.15612695X-RAY DIFFRACTION100
3.2482-3.41940.18531340.15962714X-RAY DIFFRACTION100
3.4194-3.63350.18931380.14512707X-RAY DIFFRACTION100
3.6335-3.91380.15381290.13492739X-RAY DIFFRACTION100
3.9138-4.30730.15411260.12092762X-RAY DIFFRACTION100
4.3073-4.92960.16551410.11942740X-RAY DIFFRACTION100
4.9296-6.20720.19331520.14892767X-RAY DIFFRACTION99
6.2072-40.28730.17421490.16242869X-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)
11.01370.29320.26144.5963-2.51923.22250.01690.18750.0191-0.3490.05280.10260.1062-0.1291-0.06090.14420.0320.02530.1882-0.0280.218842.170514.992532.8538
21.17510.0540.01721.0712-0.06941.0510.03430.04560.1923-0.0342-0.00630.167-0.1959-0.0765-0.02530.1830.0280.02980.15690.00740.291739.308126.967243.4991
32.10522.01942.03362.86380.48394.31590.3914-0.2617-0.06510.6004-0.3022-0.02080.30560.0174-0.09440.3622-0.12840.04760.30340.02010.252948.8876.877482.3599
41.63110.328-0.05691.5412-0.10331.57010.2309-0.420.07410.5598-0.2723-0.1434-0.16970.17490.03740.4173-0.1682-0.0340.3647-0.02460.286160.959123.167682.7376
51.6277-0.9110.57531.8839-0.72483.05960.0898-0.116-0.14880.2197-0.0916-0.25670.18230.1241-0.01570.2178-0.0721-0.02680.20380.00750.302360.21599.043971.1919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 446 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 69 )
4X-RAY DIFFRACTION4chain 'B' and (resid 70 through 365 )
5X-RAY DIFFRACTION5chain 'B' and (resid 366 through 446 )

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