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- PDB-7lqx: Crystal structure of a GH5_18 from Bifidobacterium longum subsp. ... -

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Basic information

Entry
Database: PDB / ID: 7lqx
TitleCrystal structure of a GH5_18 from Bifidobacterium longum subsp. infantis
ComponentsGlycosyl hydrolase BlGH5_18
KeywordsHYDROLASE / Glycosidase / N-glycan / CAZyme
Function / homologyGlycoside hydrolase superfamily / Glycosyl hydrolase
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsHiggins, M.A. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: N-Glycan Degradation Pathways in Gut- and Soil-Dwelling Actinobacteria Share Common Core Genes.
Authors: Higgins, M.A. / Tegl, G. / MacDonald, S.S. / Arnal, G. / Brumer, H. / Withers, S.G. / Ryan, K.S.
History
DepositionFeb 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase BlGH5_18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9978
Polymers51,4601
Non-polymers5367
Water11,908661
1
A: Glycosyl hydrolase BlGH5_18
hetero molecules

A: Glycosyl hydrolase BlGH5_18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,99416
Polymers102,9212
Non-polymers1,07314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6330 Å2
ΔGint-51 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.830, 51.720, 85.450
Angle α, β, γ (deg.)90.000, 91.240, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1171-

HOH

21A-1179-

HOH

31A-1256-

HOH

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Components

#1: Protein Glycosyl hydrolase BlGH5_18


Mass: 51460.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_2377 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7GNS6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 8 % PEG 2000, 0.2 M lithium sulfate, 0.1 M Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97911 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.3→44.4 Å / Num. obs: 95210 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 9.72 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 7.3 % / Num. unique obs: 4688 / CC1/2: 0.908 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→44.4 Å / SU ML: 0.0921 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.7407 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1518 4653 4.89 %
Rwork0.1358 90526 -
obs0.1366 95179 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.46 Å2
Refinement stepCycle: LAST / Resolution: 1.3→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 31 661 4017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553589
X-RAY DIFFRACTIONf_angle_d0.90274902
X-RAY DIFFRACTIONf_chiral_restr0.0735501
X-RAY DIFFRACTIONf_plane_restr0.0063654
X-RAY DIFFRACTIONf_dihedral_angle_d16.86951294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.21061390.2073033X-RAY DIFFRACTION99.34
1.31-1.330.2181530.20342928X-RAY DIFFRACTION99.42
1.33-1.350.18551600.20333007X-RAY DIFFRACTION99.43
1.35-1.360.23861380.19743007X-RAY DIFFRACTION99.59
1.36-1.380.21981240.18563035X-RAY DIFFRACTION99.59
1.38-1.40.19931400.18043012X-RAY DIFFRACTION99.62
1.4-1.420.20221800.17912958X-RAY DIFFRACTION99.75
1.42-1.440.20031410.17053006X-RAY DIFFRACTION99.75
1.44-1.460.18281920.15632977X-RAY DIFFRACTION99.81
1.46-1.490.16471530.15852989X-RAY DIFFRACTION99.87
1.49-1.510.15561620.15323039X-RAY DIFFRACTION99.88
1.51-1.540.17011530.14712984X-RAY DIFFRACTION99.94
1.54-1.570.17561700.14413006X-RAY DIFFRACTION100
1.57-1.60.14851510.13543004X-RAY DIFFRACTION99.97
1.6-1.640.15971250.13423026X-RAY DIFFRACTION99.94
1.64-1.680.15961620.13073020X-RAY DIFFRACTION99.97
1.68-1.720.1681540.13263027X-RAY DIFFRACTION100
1.72-1.760.13381710.1252987X-RAY DIFFRACTION99.97
1.76-1.820.15211420.12453022X-RAY DIFFRACTION99.94
1.82-1.870.15271490.12432986X-RAY DIFFRACTION99.97
1.87-1.940.13691830.12783019X-RAY DIFFRACTION100
1.94-2.020.13771610.1273013X-RAY DIFFRACTION100
2.02-2.110.13181860.1183006X-RAY DIFFRACTION100
2.11-2.220.12121510.12023044X-RAY DIFFRACTION99.97
2.22-2.360.1576980.11723081X-RAY DIFFRACTION100
2.36-2.540.13081390.1213055X-RAY DIFFRACTION100
2.54-2.80.12641770.12433016X-RAY DIFFRACTION99.97
2.8-3.210.14351820.12753050X-RAY DIFFRACTION100
3.21-4.040.1521430.1193066X-RAY DIFFRACTION100
4.04-44.40.14881740.14723123X-RAY DIFFRACTION99.91
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)
10.918448718179-0.30808324205-0.3375688318450.5250993653210.1406413531460.704635372236-0.0237003431416-0.0735275671210.01989013690670.02069022673860.0206869769502-0.030639222481-0.009658816003470.00921667454386-0.001912909868170.05190571339650.00725445022622-0.008448541119810.05617146005120.008113509864110.059502234100134.686200364154.369406048429.2752378264
20.3538261608590.4135943174320.2175447974552.09976291233-0.3794938067542.19157884681-0.0970779411766-0.0246483146346-0.1078981010.01836867335130.02124122187970.02676044482570.153297631053-0.1347187131770.08390882167410.05456801542260.01176286855960.00137862105130.06393643664030.02283025144190.095014498719839.130008859138.129217468419.2125074664
30.7135340841710.033656650486-0.3679745712130.459062024181-0.1831793469861.16931164113-0.04886463717210.0538193943882-0.093244878689-0.0008246882521360.00404663087520.01812163453970.103069358404-0.1078445770280.03296445849050.0565782463025-0.006744502097550.003917903264840.0744800681301-0.0132002500210.084545616079533.928253923644.8735603739.24901041852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 174 through 420 )A174 - 420
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 24 )A1 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 173 )A25 - 173

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