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- PDB-5oo2: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

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Basic information

Entry
Database: PDB / ID: 5oo2
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) E419A variant in complex with glucosylglycolate
ComponentsUncharacterized protein
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
(alpha-D-glucopyranosyloxy)acetic acid / SERINE / Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 5, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)103,39316
Polymers101,7992
Non-polymers1,59514
Water7,674426
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,78732
Polymers203,5984
Non-polymers3,18928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area13670 Å2
ΔGint-27 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.953, 157.676, 87.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-818-

HOH

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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)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / 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.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-9YW / (alpha-D-glucopyranosyloxy)acetic acid / Glucosylglycolate / (alpha-D-glucosyloxy)acetic acid / (D-glucosyloxy)acetic acid / (glucosyloxy)acetic acid


Type: D-saccharide / Mass: 238.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O8
#4: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.06→45.06 Å / Num. obs: 75133 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.052 / Rrim(I) all: 0.135 / Net I/σ(I): 8.2
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.575 / Rpim(I) all: 0.579 / Rrim(I) all: 1.526 / % 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: 2.06→41.912 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 3625 4.83 %
Rwork0.1622 --
obs0.1642 75046 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→41.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 105 426 7689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017668
X-RAY DIFFRACTIONf_angle_d1.0310458
X-RAY DIFFRACTIONf_dihedral_angle_d20.0784507
X-RAY DIFFRACTIONf_chiral_restr0.0591077
X-RAY DIFFRACTIONf_plane_restr0.0071370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.08710.3181460.27932724X-RAY DIFFRACTION100
2.0871-2.11570.29521400.26312687X-RAY DIFFRACTION100
2.1157-2.14590.2992950.25612751X-RAY DIFFRACTION100
2.1459-2.1780.30541340.25592727X-RAY DIFFRACTION100
2.178-2.2120.2871240.23862720X-RAY DIFFRACTION100
2.212-2.24820.29971280.23042736X-RAY DIFFRACTION100
2.2482-2.2870.29091470.22592731X-RAY DIFFRACTION100
2.287-2.32860.30321250.21132710X-RAY DIFFRACTION100
2.3286-2.37340.25991730.20652696X-RAY DIFFRACTION100
2.3734-2.42180.24881500.19332700X-RAY DIFFRACTION100
2.4218-2.47450.25111310.19182729X-RAY DIFFRACTION100
2.4745-2.5320.2391190.18262739X-RAY DIFFRACTION100
2.532-2.59530.23931270.18312730X-RAY DIFFRACTION100
2.5953-2.66550.23191190.17352771X-RAY DIFFRACTION100
2.6655-2.74390.20081520.17162717X-RAY DIFFRACTION100
2.7439-2.83250.231350.16172734X-RAY DIFFRACTION100
2.8325-2.93370.17431380.15182742X-RAY DIFFRACTION100
2.9337-3.05110.21711290.15952754X-RAY DIFFRACTION100
3.0511-3.18990.19941480.15172735X-RAY DIFFRACTION100
3.1899-3.3580.18541560.15882760X-RAY DIFFRACTION100
3.358-3.56830.19341410.14752736X-RAY DIFFRACTION100
3.5683-3.84370.17711740.1342752X-RAY DIFFRACTION100
3.8437-4.23010.16091230.12792788X-RAY DIFFRACTION100
4.2301-4.84150.16261310.12362794X-RAY DIFFRACTION99
4.8415-6.09670.19961740.15742808X-RAY DIFFRACTION100
6.0967-41.92110.17331660.16292950X-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)
10.958-0.34210.00795.42143.05324.6211-0.0071-0.28110.03990.73720.0141-0.13630.10130.15730.0020.3519-0.0416-0.00910.26110.02980.2576-43.440515.4973-30.7218
22.16990.76860.40432.46080.20631.9238-0.0216-0.18980.14730.3415-0.0349-0.2404-0.32930.12220.06310.4025-0.0067-0.01020.2387-0.03280.3013-43.851330.5217-36.2683
31.8601-0.13370.71372.5536-0.26642.2811-0.01280.12170.1096-0.0677-0.0434-0.3771-0.16810.30660.05860.2463-0.05040.0440.2546-0.01340.3144-34.756621.4633-50.9892
41.368-1.87871.66577.1081-3.1216.09820.28720.308-0.1873-0.7702-0.12620.33640.3456-0.1624-0.14150.31810.0766-0.01230.2981-0.05510.2999-49.77776.4371-80.217
55.3967-0.57893.37271.06-0.09477.18830.33651.049-0.1386-0.4868-0.25010.1068-0.1725-0.053-0.10280.50670.16780.01170.4693-0.02930.3096-53.738719.257-89.449
67.7913-0.979-0.60671.9791-0.07351.61030.18790.58250.2929-0.4643-0.17840.08-0.4153-0.1756-0.00750.53320.1384-0.01190.38270.02250.2256-58.254125.9477-82.327
70.10170.0936-0.14290.2383-0.20040.2315-0.5303-1.31750.54610.09860.095-0.47590.3143-1.22880.30621.01860.0854-0.27431.4394-0.171.0701-73.78176.5028-91.2702
83.10642.3265-0.69814.10413.89668.95750.20451.2492-0.1873-0.171-0.24650.18730.0012-0.793-0.00360.6980.3405-0.2480.9165-0.08090.6243-71.800723.3279-93.9481
94.02150.6734-1.10411.5194-0.21661.95310.20440.22340.3114-0.147-0.16790.2066-0.4556-0.2124-0.04190.4790.1437-0.02350.29060.00890.3171-61.327330.8931-73.3035
103.1641-0.5522-0.18763.42920.95982.38640.03580.0822-0.3508-0.0227-0.1020.33910.0424-0.23570.07010.25120.0222-0.01680.26310.00540.3037-63.38611.5134-66.6291
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 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 446 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 69 )
5X-RAY DIFFRACTION5chain 'B' and (resid 70 through 134 )
6X-RAY DIFFRACTION6chain 'B' and (resid 135 through 193 )
7X-RAY DIFFRACTION7chain 'B' and (resid 194 through 218 )
8X-RAY DIFFRACTION8chain 'B' and (resid 219 through 249 )
9X-RAY DIFFRACTION9chain 'B' and (resid 250 through 320 )
10X-RAY DIFFRACTION10chain 'B' and (resid 321 through 446 )

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