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- PDB-5oi0: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

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Basic information

Entry
Database: PDB / ID: 5oi0
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) in complex with serine and glycerol
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
SERINE / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,32217
Polymers101,9152
Non-polymers1,40715
Water15,097838
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,64534
Polymers203,8304
Non-polymers2,81530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15040 Å2
ΔGint-29 kcal/mol
Surface area59460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.981, 158.802, 87.827
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: 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


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
Details: Two serine molecules (chain E and chain F) with two alternative conformations (altid A and altid B) are present in the active sites (one per active site). Serine is one of the components of ...Details: Two serine molecules (chain E and chain F) with two alternative conformations (altid A and altid B) are present in the active sites (one per active site). Serine is one of the components of the crystallization condition.
#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.: 838 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
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: ID30B / Wavelength: 0.97265 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97265 Å / Relative weight: 1
ReflectionResolution: 1.68→48.591 Å / Num. obs: 135623 / % possible obs: 99 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.025 / Rrim(I) all: 0.053 / Net I/σ(I): 16.4
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.637 / Rpim(I) all: 0.444 / Rrim(I) all: 0.972 / % possible all: 98.4

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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: 1.68→48.591 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1723 6808 5.02 %
Rwork0.1458 --
obs0.1471 135565 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→48.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7166 0 92 838 8096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018014
X-RAY DIFFRACTIONf_angle_d1.03110959
X-RAY DIFFRACTIONf_dihedral_angle_d19.8644736
X-RAY DIFFRACTIONf_chiral_restr0.0631106
X-RAY DIFFRACTIONf_plane_restr0.0081459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.69910.31092020.26864173X-RAY DIFFRACTION97
1.6991-1.71910.30192260.2584246X-RAY DIFFRACTION99
1.7191-1.740.23322110.23684252X-RAY DIFFRACTION99
1.74-1.76210.26341970.22034328X-RAY DIFFRACTION99
1.7621-1.78530.23512000.21174244X-RAY DIFFRACTION99
1.7853-1.80970.24042210.2114266X-RAY DIFFRACTION99
1.8097-1.83560.21192230.20164263X-RAY DIFFRACTION99
1.8356-1.8630.23162390.19564209X-RAY DIFFRACTION98
1.863-1.89210.20152130.18244222X-RAY DIFFRACTION98
1.8921-1.92310.20522500.16924254X-RAY DIFFRACTION99
1.9231-1.95630.19422260.16674232X-RAY DIFFRACTION98
1.9563-1.99180.21562410.16524156X-RAY DIFFRACTION97
1.9918-2.03020.17932270.15164271X-RAY DIFFRACTION99
2.0302-2.07160.18972330.14924281X-RAY DIFFRACTION99
2.0716-2.11660.17852110.14514320X-RAY DIFFRACTION99
2.1166-2.16590.16592100.1464290X-RAY DIFFRACTION99
2.1659-2.220.18062650.13854263X-RAY DIFFRACTION99
2.22-2.28010.18782090.14184337X-RAY DIFFRACTION100
2.2801-2.34720.19422340.13724276X-RAY DIFFRACTION99
2.3472-2.42290.16512220.14694320X-RAY DIFFRACTION99
2.4229-2.50950.17952300.14474279X-RAY DIFFRACTION98
2.5095-2.610.1792310.14514261X-RAY DIFFRACTION98
2.61-2.72880.16032350.14084310X-RAY DIFFRACTION100
2.7288-2.87260.18382520.14184339X-RAY DIFFRACTION100
2.8726-3.05260.15422200.13544369X-RAY DIFFRACTION100
3.0526-3.28820.14612460.13084363X-RAY DIFFRACTION100
3.2882-3.6190.14732410.12724332X-RAY DIFFRACTION99
3.619-4.14240.1352160.11514336X-RAY DIFFRACTION98
4.1424-5.21810.1492550.12154440X-RAY DIFFRACTION100
5.2181-48.61180.18972220.17074525X-RAY DIFFRACTION97
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)
10.99170.58490.42343.8594-1.56742.85650.0150.0467-0.0906-0.18030.02840.17720.0288-0.0854-0.03690.15250.0189-0.00010.1165-0.02520.178541.93289.299437.7027
22.6808-0.79481.40341.8251-0.84353.48520.13740.3115-0.0147-0.4512-0.09650.02090.02510.0587-0.06760.24450.01520.02280.1447-0.0110.156246.592921.329428.2862
31.306-0.10920.03951.1357-0.12791.10230.03130.14930.1976-0.1944-0.00970.065-0.2118-0.0075-0.00790.23240.01240.0080.14250.02730.196143.693330.444634.4189
43.69990.3621.70742.4287-3.20227.2183-0.0624-0.07650.4880.13080.04410.2239-0.8302-0.34180.01570.3980.1350.04920.1925-0.01790.412133.419841.566445.8835
51.18270.25230.29941.3460.01781.10940.0251-0.09950.08460.09060.00040.2711-0.1014-0.1761-0.01920.14740.02170.02940.15050.00610.208133.95921.261150.8065
61.58861.36781.34553.10480.89153.62360.1993-0.2461-0.1620.2808-0.1498-0.05770.14860.0871-0.04790.1907-0.07740.01050.25710.03450.179549.24237.008380.2081
71.7935-0.04080.63181.21020.08662.8290.1713-0.56260.04210.3743-0.19360.0581-0.1136-0.10610.00560.3086-0.1270.05140.374-0.04260.192349.957321.967987.5972
84.413-1.6432.01912.652-1.74042.95230.0753-0.37430.10320.398-0.1529-0.4166-0.29470.2570.04370.2675-0.1457-0.04330.38950.01150.222769.165625.174282.3339
91.22320.64690.74333.62011.69993.28040.2212-0.5269-0.09860.5681-0.1986-0.3972-0.01380.3724-0.0610.3751-0.1875-0.14670.61480.09970.354771.62116.813792.8124
100.83140.2142-0.01541.2783-0.13731.21630.0906-0.089-0.01410.0427-0.1081-0.1829-0.10160.17040.00910.1557-0.0472-0.00650.2078-0.00040.177261.460819.210969.259
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 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 320 )
5X-RAY DIFFRACTION5chain 'A' and (resid 321 through 446 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 69 )
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 162 )
8X-RAY DIFFRACTION8chain 'B' and (resid 163 through 193 )
9X-RAY DIFFRACTION9chain 'B' and (resid 194 through 249 )
10X-RAY DIFFRACTION10chain 'B' and (resid 250 through 446 )

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