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- PDB-5oi1: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

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Basic information

Entry
Database: PDB / ID: 5oi1
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with serine and glycerol
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
SERINE / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 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)103,05015
Polymers101,8272
Non-polymers1,22313
Water13,980776
1
A: Hydrolase
B: Hydrolase
hetero molecules

A: Hydrolase
B: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,10030
Polymers203,6544
Non-polymers2,44626
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)86.286, 158.046, 87.654
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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SER / SERINE


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


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
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: 1.75→42.23 Å / Num. obs: 119738 / % possible obs: 98.8 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.035 / Rrim(I) all: 0.079 / Net I/σ(I): 11.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5 % / Rmerge(I) obs: 0.987 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.579 / Rpim(I) all: 0.48 / Rrim(I) all: 1.102 / % possible all: 99.3

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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: 1.75→40.007 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1719 5953 4.97 %
Rwork0.1462 --
obs0.1475 119673 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→40.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 80 776 8016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017896
X-RAY DIFFRACTIONf_angle_d1.01910794
X-RAY DIFFRACTIONf_dihedral_angle_d18.9594657
X-RAY DIFFRACTIONf_chiral_restr0.0651093
X-RAY DIFFRACTIONf_plane_restr0.0071433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.28021890.2593755X-RAY DIFFRACTION99
1.7699-1.79070.29952120.24963777X-RAY DIFFRACTION99
1.7907-1.81250.25771930.24713763X-RAY DIFFRACTION99
1.8125-1.83550.26551980.22563796X-RAY DIFFRACTION99
1.8355-1.85960.26291940.21753768X-RAY DIFFRACTION99
1.8596-1.88510.24232000.20093774X-RAY DIFFRACTION100
1.8851-1.9120.22621930.19733785X-RAY DIFFRACTION100
1.912-1.94060.20652200.18343768X-RAY DIFFRACTION100
1.9406-1.97090.21542250.17733759X-RAY DIFFRACTION100
1.9709-2.00320.18841880.16963846X-RAY DIFFRACTION100
2.0032-2.03780.22771970.15823788X-RAY DIFFRACTION100
2.0378-2.07480.19441930.15773814X-RAY DIFFRACTION100
2.0748-2.11470.18672080.15383792X-RAY DIFFRACTION100
2.1147-2.15790.19642280.15133793X-RAY DIFFRACTION100
2.1579-2.20480.16452220.13943791X-RAY DIFFRACTION100
2.2048-2.25610.15881700.13793808X-RAY DIFFRACTION100
2.2561-2.31250.17011590.13843860X-RAY DIFFRACTION100
2.3125-2.3750.16291830.1393820X-RAY DIFFRACTION99
2.375-2.44490.19891940.14283784X-RAY DIFFRACTION99
2.4449-2.52380.16591880.14293758X-RAY DIFFRACTION98
2.5238-2.6140.16391750.14713497X-RAY DIFFRACTION90
2.614-2.71860.20831320.14073398X-RAY DIFFRACTION88
2.7186-2.84230.17811950.14413802X-RAY DIFFRACTION99
2.8423-2.99210.18362320.13953803X-RAY DIFFRACTION100
2.9921-3.17950.15622150.1343847X-RAY DIFFRACTION99
3.1795-3.42490.15852440.13413809X-RAY DIFFRACTION99
3.4249-3.76930.15041960.12333877X-RAY DIFFRACTION99
3.7693-4.31420.12982030.11423891X-RAY DIFFRACTION99
4.3142-5.43330.14562020.12883935X-RAY DIFFRACTION99
5.4333-40.01760.16712050.17064062X-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)
10.9753-0.59570.25614.3111.42053.61170.003-0.0447-0.08340.22540.0291-0.15050.07650.0921-0.02510.1441-0.0165-0.00410.10720.02280.1726-42.2859.3142-37.4446
26.0903-0.34320.66972.79520.57585.31540.0199-0.7356-0.10290.79040.016-0.02060.1420.0019-0.01110.4118-0.0463-0.00830.2029-0.01190.1777-43.756123.6426-22.2478
31.1570.1129-0.02711.20060.07311.11860.0099-0.05690.1610.12440.0057-0.1075-0.22480.0444-0.01150.2171-0.0121-0.00580.1269-0.01410.2079-41.818130.1741-39.7763
41.5199-0.18790.5381.19550.08541.60260.00030.04250.012-0.00350.0276-0.2585-0.05640.1627-0.04460.142-0.01660.01610.1224-0.01050.2113-34.398117.4708-48.3931
51.3693-1.78891.65264.0764-1.27543.91720.17230.1798-0.1468-0.2974-0.14870.05750.132-0.095-0.02820.16820.06530.01010.2349-0.03320.1677-49.36496.8755-80.1118
62.4729-0.04821.99980.94710.02365.04550.25680.6772-0.0365-0.4073-0.22340.0088-0.01610.0797-0.07280.33940.15320.01620.39140.01450.1971-52.94719.3539-89.4078
71.0879-0.2512-0.09441.24150.04121.38790.10370.2362-0.0184-0.191-0.12680.2153-0.1426-0.21990.00990.19860.08-0.03410.2534-0.01180.1992-62.774919.9315-75.8147
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 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 365 )
4X-RAY DIFFRACTION4chain 'A' and (resid 366 through 446 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 134 )
7X-RAY DIFFRACTION7chain 'B' and (resid 135 through 446 )

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