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- PDB-5oj4: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

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Basic information

Entry
Database: PDB / ID: 5oj4
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with mannosylglycerate
ComponentsHydrolase
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
Chem-2M8 / GLYCINE / DI(HYDROXYETHYL)ETHER / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.2May 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 1.3Jul 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)104,21324
Polymers101,8272
Non-polymers2,38622
Water15,241846
1
A: Hydrolase
B: Hydrolase
hetero molecules

A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,42748
Polymers203,6544
Non-polymers4,77344
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)85.329, 159.632, 91.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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 DSM 44199 (bacteria)
Gene: C731_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDL0
#5: Sugar ChemComp-2M8 / (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid / 2-O-ALPHA-MANNOSYL-D-GLYCERATE / (2R)-3-hydroxy-2-(alpha-D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(D-mannosyloxy)propanoic acid / (2R)-3-hydroxy-2-(mannosyloxy)propanoic acid


Type: D-saccharide, alpha linking / Mass: 268.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O9

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Non-polymers , 4 types, 866 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 59.79 %
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-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.79→49.11 Å / Num. obs: 117039 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 16.5
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.66 / Rpim(I) all: 0.436 / Rrim(I) all: 1.141 / % possible all: 95.9

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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: 1.79→49.11 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1729 5861 5.01 %
Rwork0.144 --
obs0.1454 116974 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 157 846 8163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017800
X-RAY DIFFRACTIONf_angle_d0.98610626
X-RAY DIFFRACTIONf_dihedral_angle_d19.8644600
X-RAY DIFFRACTIONf_chiral_restr0.0621087
X-RAY DIFFRACTIONf_plane_restr0.0071393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.81030.29732020.28273496X-RAY DIFFRACTION95
1.8103-1.83160.30581810.25743498X-RAY DIFFRACTION96
1.8316-1.8540.28941920.24473566X-RAY DIFFRACTION97
1.854-1.87740.22991730.22043630X-RAY DIFFRACTION98
1.8774-1.90220.22422060.20563589X-RAY DIFFRACTION98
1.9022-1.92820.24541870.20513657X-RAY DIFFRACTION99
1.9282-1.95580.22652170.19073668X-RAY DIFFRACTION100
1.9558-1.9850.21562240.18643666X-RAY DIFFRACTION100
1.985-2.0160.20191950.17593700X-RAY DIFFRACTION100
2.016-2.0490.18872160.16083631X-RAY DIFFRACTION100
2.049-2.08440.18481830.15673724X-RAY DIFFRACTION100
2.0844-2.12230.18221800.1553719X-RAY DIFFRACTION100
2.1223-2.16310.18722030.14953681X-RAY DIFFRACTION100
2.1631-2.20720.17191950.14333687X-RAY DIFFRACTION100
2.2072-2.25520.20481970.14393701X-RAY DIFFRACTION100
2.2552-2.30770.16121780.13813745X-RAY DIFFRACTION100
2.3077-2.36540.15461860.13523702X-RAY DIFFRACTION100
2.3654-2.42930.18862010.14323701X-RAY DIFFRACTION100
2.4293-2.50080.17082040.1373709X-RAY DIFFRACTION100
2.5008-2.58150.17382090.14243724X-RAY DIFFRACTION100
2.5815-2.67380.19031940.14073719X-RAY DIFFRACTION100
2.6738-2.78080.17831940.13693742X-RAY DIFFRACTION100
2.7808-2.90740.16072170.13713708X-RAY DIFFRACTION100
2.9074-3.06070.16322000.13453764X-RAY DIFFRACTION100
3.0607-3.25240.16331900.1323732X-RAY DIFFRACTION100
3.2524-3.50340.16721910.13093753X-RAY DIFFRACTION100
3.5034-3.85590.13731680.12033814X-RAY DIFFRACTION100
3.8559-4.41350.12811840.11023829X-RAY DIFFRACTION100
4.4135-5.55930.14662020.12793829X-RAY DIFFRACTION100
5.5593-49.12870.1841920.16664029X-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)
10.5080.29060.80083.8772-0.9473.10810.01120.0127-0.0734-0.13060.06680.09480.0706-0.0869-0.06330.07870.01250.00970.119-0.01510.169641.74478.727339.3349
20.80780.01210.05481.094-0.10861.20810.01120.07130.1158-0.07730.00960.1102-0.2365-0.067-0.01840.17350.01820.00880.12840.0140.192539.871726.518641.2196
31.94481.12991.37441.95970.91043.35360.1808-0.3115-0.05760.4911-0.1701-0.05120.08280.0932-0.00770.3236-0.0920.00910.26450.03160.1752.046511.672388.1979
41.43210.19410.06851.322-0.07181.40640.1292-0.25230.0760.3716-0.1477-0.1975-0.23980.23980.0260.3488-0.1215-0.03710.2732-0.00610.192460.111324.871783.417
51.0045-0.04880.25672.4553-0.89981.92910.07410.0065-0.09910.0251-0.108-0.25760.06090.26710.02250.1478-0.0241-0.01320.1934-0.01090.185362.120512.16568.6728
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 446 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 117 )
4X-RAY DIFFRACTION4chain 'B' and (resid 118 through 320 )
5X-RAY DIFFRACTION5chain 'B' and (resid 321 through 446 )

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