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- PDB-6q5t: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -

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Basic information

Entry
Database: PDB / ID: 6q5t
TitleCrystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) - apo form
Componentshydrolase
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
Glucosylglycerate hydrolase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsCereija, T.B. / Macedo-Ribeiro, S. / Pereira, P.J.B.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia (POCI-01-0145-FEDER-007274) Portugal
Norte Portugal Regional Operational Programme NORTE 2020 (Norte-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
DepositionDec 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: pdbx_related_exp_data_set
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 1.3Jan 24, 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


Theoretical massNumber of molelcules
Total (without water)101,9152
Polymers101,9152
Non-polymers00
Water6,828379
1
A: hydrolase
B: hydrolase

A: hydrolase
B: hydrolase


Theoretical massNumber of molelcules
Total (without water)203,8304
Polymers203,8304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area8400 Å2
ΔGint-32 kcal/mol
Surface area64120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.008, 167.008, 243.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-557-

HOH

21B-702-

HOH

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Components

#1: Protein hydrolase /


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 4.82 Å3/Da / Density % sol: 74.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ADA pH 6.5, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.54→49.86 Å / Num. obs: 66272 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.043 / Rrim(I) all: 0.117 / Rsym value: 0.109 / Net I/σ(I): 11.9
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.165 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.673 / Rpim(I) all: 0.459 / Rrim(I) all: 1.254 / Rsym value: 1.165 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHZ
Resolution: 2.54→49.86 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.77
RfactorNum. reflection% reflection
Rfree0.2038 3359 5.08 %
Rwork0.1663 --
obs0.1682 66183 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7088 0 0 379 7467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097480
X-RAY DIFFRACTIONf_angle_d1.05810202
X-RAY DIFFRACTIONf_dihedral_angle_d22.2654403
X-RAY DIFFRACTIONf_chiral_restr0.0591050
X-RAY DIFFRACTIONf_plane_restr0.0071342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.57630.33161410.29742551X-RAY DIFFRACTION100
2.5763-2.61480.36191460.27862577X-RAY DIFFRACTION100
2.6148-2.65560.33981420.27512558X-RAY DIFFRACTION100
2.6556-2.69920.31021260.26352587X-RAY DIFFRACTION99
2.6992-2.74570.27831420.24562549X-RAY DIFFRACTION100
2.7457-2.79560.30821200.22242609X-RAY DIFFRACTION100
2.7956-2.84940.29191200.22862588X-RAY DIFFRACTION100
2.8494-2.90750.25821500.23072579X-RAY DIFFRACTION100
2.9075-2.97080.30741420.23182574X-RAY DIFFRACTION100
2.9708-3.03980.28671250.2282631X-RAY DIFFRACTION100
3.0398-3.11590.29311390.23122572X-RAY DIFFRACTION100
3.1159-3.20010.241360.20362601X-RAY DIFFRACTION100
3.2001-3.29420.21221610.17992576X-RAY DIFFRACTION100
3.2942-3.40050.21461390.16862605X-RAY DIFFRACTION100
3.4005-3.52210.21481630.16482581X-RAY DIFFRACTION100
3.5221-3.6630.19181400.14192597X-RAY DIFFRACTION100
3.663-3.82970.16981410.12842629X-RAY DIFFRACTION100
3.8297-4.03150.15651610.11692604X-RAY DIFFRACTION100
4.0315-4.2840.14891390.10682657X-RAY DIFFRACTION100
4.284-4.61450.13351160.10422658X-RAY DIFFRACTION100
4.6145-5.07850.14671370.11432669X-RAY DIFFRACTION100
5.0785-5.81240.16291470.14532687X-RAY DIFFRACTION100
5.8124-7.31930.21031540.17082704X-RAY DIFFRACTION99
7.3193-49.87140.18311320.18712881X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.8866-3.5695-6.16153.21834.12066.58790.03310.2614-0.29520.0682-0.35010.4188-0.1295-0.91470.31840.41240.0866-0.05910.61730.08760.429318.815278.032733.354
28.4184-0.9216-4.22531.24530.24323.52830.10180.52170.2736-0.11120.07140.1141-0.433-0.4373-0.15950.45570.11990.04550.47980.10330.41213.885787.849650.9005
38.11441.242-6.23976.4753-1.58477.99770.3809-0.04010.53620.1737-0.1337-0.318-0.77840.4649-0.23720.36640.0094-0.04070.3620.05980.466929.964890.000452.5766
47.77292.45971.05654.37640.29133.79340.0211-0.2075-0.14120.45420.03490.18550.2368-0.0778-0.01530.42850.07980.15760.43030.08160.343713.341572.521263.1788
57.97033.8902-7.28082.3564-2.68298.51240.20011.20050.7482-0.1528-0.0020.8446-0.5656-0.9106-0.04960.61150.06850.02880.91380.02080.7767-2.92975.054553.1884
63.81220.1017-0.77991.7973-0.23632.0117-0.0716-0.3798-0.09380.16740.0275-0.04530.15950.07970.04390.46110.0790.05230.49940.04140.293219.73676.378864.7587
74.33850.69661.07222.32020.25184.2631-0.1113-0.0571-0.2839-0.0522-0.0037-0.04860.58460.12310.11210.39350.10690.0940.35150.04520.347325.738564.024548.1316
84.1642-1.74092.26082.9234-0.79895.0425-0.2491-0.43090.21380.02770.0105-0.2244-0.3197-0.05460.2150.32410.1010.03670.47950.08210.370125.027385.632523.2788
93.168-1.09930.37635.0331-0.75912.9196-0.0197-0.0119-0.235-0.14360.0470.26810.2605-0.1297-0.04520.34160.0073-0.0340.35650.04910.344915.544783.52037.093
102.43090.76430.63964.2239-1.06623.881-0.0660.11210.53730.0563-0.01720.4617-0.3679-0.19780.07150.47120.0481-0.07880.41890.08820.524722.5584102.89432.1647
111.8637-0.2548-0.01912.4124-0.60241.57950.01610.2049-0.0064-0.4304-0.1242-0.09350.11790.22650.10920.56210.0847-0.00920.47860.04210.308426.536489.5806-4.2309
122.06270.1877-0.2282.48150.2272.730.0025-0.1069-0.1264-0.0793-0.1516-0.28620.09790.55470.14450.33640.0794-0.00660.49990.10530.382940.536690.348112.4672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 193 )
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 221 )
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 320 )
7X-RAY DIFFRACTION7chain 'A' and (resid 321 through 446 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 69 )
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 162 )
10X-RAY DIFFRACTION10chain 'B' and (resid 163 through 221 )
11X-RAY DIFFRACTION11chain 'B' and (resid 222 through 320 )
12X-RAY DIFFRACTION12chain 'B' and (resid 321 through 446 )

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