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

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Basic information

Entry
Database: PDB / ID: 5ont
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase(MhGgH) E419A variant in complex with glucosylglycerol
ComponentsUncharacterized protein
KeywordsHYDROLASE / Mycobacterium
Function / homology
Function and homology information


glucosylglycerate hydrolase / glucosylglycerate hydrolase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation
Similarity search - Function
: / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / 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
1,3-dihydroxypropan-2-yl alpha-D-glucopyranoside / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04412
Polymers101,7992
Non-polymers1,24510
Water10,196566
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,08824
Polymers203,5984
Non-polymers2,49020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12480 Å2
ΔGint-23 kcal/mol
Surface area60590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.898, 158.760, 87.720
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 Uncharacterized protein


Mass: 50899.461 Da / Num. of mol.: 2 / Mutation: E419A
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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-A0K / 1,3-dihydroxypropan-2-yl alpha-D-glucopyranoside / (2~{S},3~{R},4~{S},5~{S},6~{R})-2-[1,3-bis(oxidanyl)propan-2-yloxy]-6-(hydroxymethyl)oxane-3,4,5-triol / 1,3-dihydroxypropan-2-yl alpha-D-glucoside / 1,3-dihydroxypropan-2-yl D-glucoside / 1,3-dihydroxypropan-2-yl glucoside


Type: D-saccharide / Mass: 254.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
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: 2.05→45.313 Å / Num. obs: 76309 / % possible obs: 99.4 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.049 / Rrim(I) all: 0.104 / Net I/σ(I): 9.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.901 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.552 / Rpim(I) all: 0.488 / Rrim(I) all: 1.027 / % possible all: 100

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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: 2.05→45.313 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.33
RfactorNum. reflection% reflection
Rfree0.195 3909 5.13 %
Rwork0.1542 --
obs0.1563 76246 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→45.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7055 0 82 566 7703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017610
X-RAY DIFFRACTIONf_angle_d1.01110387
X-RAY DIFFRACTIONf_dihedral_angle_d19.3194471
X-RAY DIFFRACTIONf_chiral_restr0.0591067
X-RAY DIFFRACTIONf_plane_restr0.0071361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.0750.32141630.26442551X-RAY DIFFRACTION100
2.075-2.10130.2951450.24522563X-RAY DIFFRACTION100
2.1013-2.12890.30161190.24032615X-RAY DIFFRACTION100
2.1289-2.15810.24691300.22662539X-RAY DIFFRACTION100
2.1581-2.18890.28261520.21362568X-RAY DIFFRACTION100
2.1889-2.22160.23811210.19792566X-RAY DIFFRACTION100
2.2216-2.25630.26731040.19452620X-RAY DIFFRACTION100
2.2563-2.29330.26391540.19192574X-RAY DIFFRACTION100
2.2933-2.33290.20021500.1822556X-RAY DIFFRACTION100
2.3329-2.37530.23251500.17462558X-RAY DIFFRACTION100
2.3753-2.4210.22331410.17172559X-RAY DIFFRACTION99
2.421-2.47040.20041330.16452525X-RAY DIFFRACTION99
2.4704-2.52410.22261300.1652549X-RAY DIFFRACTION98
2.5241-2.58280.20611480.16162556X-RAY DIFFRACTION99
2.5828-2.64740.20061070.15792608X-RAY DIFFRACTION99
2.6474-2.7190.20911210.15122584X-RAY DIFFRACTION99
2.719-2.79890.23321240.1572613X-RAY DIFFRACTION100
2.7989-2.88930.22451120.1482578X-RAY DIFFRACTION99
2.8893-2.99250.19581130.15622551X-RAY DIFFRACTION97
2.9925-3.11230.17571550.15212409X-RAY DIFFRACTION93
3.1123-3.25390.19331560.14382534X-RAY DIFFRACTION98
3.2539-3.42540.17291490.14642586X-RAY DIFFRACTION100
3.4254-3.63990.15871470.13752616X-RAY DIFFRACTION100
3.6399-3.92080.17991680.12892604X-RAY DIFFRACTION100
3.9208-4.31510.15121570.11512614X-RAY DIFFRACTION100
4.3151-4.93890.18741430.11932658X-RAY DIFFRACTION100
4.9389-6.21990.1831550.1552688X-RAY DIFFRACTION100
6.2199-45.32380.1751620.16722795X-RAY DIFFRACTION100
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)
10.96271.3537-0.22695.7274-2.65314.9661-0.04970.1231-0.0351-0.28980.15410.23350.0673-0.2011-0.0840.15770.01740.00520.1553-0.03020.213142.51139.076737.3997
23.6563-1.92022.33473.2549-2.38216.66620.16120.39510.0097-0.627-0.13410.009-0.0032-0.0819-0.06580.3191-0.00770.02680.1869-0.02630.212846.640721.382328.1304
33.2281-1.25620.34462.3927-0.32431.68440.03850.29770.0809-0.3606-0.05130.2637-0.248-0.11160.00580.322-0.0049-0.01480.20050.01390.239141.133830.15732.4584
41.25070.1323-0.0911.69690.09051.13830.0022-0.06890.13820.05670.01320.3078-0.2101-0.1533-0.02550.2280.03070.00690.1913-0.00080.249337.873825.881449.1548
51.46232.27641.7375.69781.93785.54470.2792-0.2362-0.1590.5843-0.1067-0.22590.2840.234-0.1580.2511-0.04720.0060.28810.02880.215249.62186.519580.3654
62.28220.4841-0.21491.5123-0.10171.93020.1879-0.58160.00220.4581-0.2412-0.215-0.22960.32920.05360.4387-0.1458-0.04450.42430.00090.245660.658524.308483.9707
71.82220.4103-0.0773.0532-0.8721.77430.0519-0.0612-0.23740.0213-0.1307-0.36890.05110.26730.06790.188-0.0231-0.0210.25810.00310.229663.270711.947366.8926
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 272 )
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 446 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 320 )
7X-RAY DIFFRACTION7chain 'B' and (resid 321 through 446 )

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