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- PDB-6nob: Structure of Glycoside Hydrolase family 32 from Bifidobacterium a... -

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Basic information

Entry
Database: PDB / ID: 6nob
TitleStructure of Glycoside Hydrolase family 32 from Bifidobacterium adolescentis
ComponentsBeta-fructofuranosidaseSucrase
KeywordsHYDROLASE / GH32 / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-fructofuranosidase
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsMera, A.M. / Lima, M.Z.T. / Muniz, J.R.C.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/16291-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)486546/2013-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)309767/2015-6 Brazil
CitationJournal: To Be Published
Title: Structure of GH32 from Bifidobacterium adolescentis
Authors: Mera, A. / Lima, M.Z.T. / Bernardes, A. / Garcia, W. / Muniz, J.R.C.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7898
Polymers70,2221
Non-polymers5677
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-fructofuranosidase
hetero molecules

A: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,57716
Polymers140,4442
Non-polymers1,13314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area6480 Å2
ΔGint30 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.903, 130.903, 132.937
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1163-

HOH

21A-1250-

HOH

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Components

#1: Protein Beta-fructofuranosidase / Sucrase


Mass: 70221.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a) (bacteria)
Strain: ATCC 15703 / DSM 20083 / NCTC 11814 / E194a / Gene: BAD_1325 / Production host: Escherichia coli (E. coli) / References: UniProt: A1A323
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 4.7 Å3/Da / Density % sol: 73.85 % / Description: hexagonal crystals
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 8K 25% (w/v), MES 0.1M pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45866 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45866 Å / Relative weight: 1
ReflectionResolution: 2.44→57.34 Å / Num. obs: 49401 / % possible obs: 100 % / Redundancy: 18.4 % / Biso Wilson estimate: 42.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.282 / Rrim(I) all: 0.298 / Net I/σ(I): 9.9
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 15.1 % / Rmerge(I) obs: 3.425 / Mean I/σ(I) obs: 1 / Num. unique obs: 54042 / CC1/2: 0.669 / Rpim(I) all: 0.926 / Rrim(I) all: 3.67 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
TRUNCATEdata reduction
Aimlessdata scaling
DIALSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UYP

1uyp


Resolution: 2.44→52.14 Å / SU ML: 0.2749 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4693
RfactorNum. reflection% reflection
Rfree0.2098 2458 4.99 %
Rwork0.1766 --
obs0.1783 49281 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.94 Å2
Refinement stepCycle: LAST / Resolution: 2.44→52.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 37 374 5317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235090
X-RAY DIFFRACTIONf_angle_d0.57436919
X-RAY DIFFRACTIONf_chiral_restr0.0452733
X-RAY DIFFRACTIONf_plane_restr0.0034929
X-RAY DIFFRACTIONf_dihedral_angle_d7.11764058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.490.32371080.27752577X-RAY DIFFRACTION99.59
2.49-2.540.27931360.26492563X-RAY DIFFRACTION99.78
2.54-2.590.30461220.26342594X-RAY DIFFRACTION99.74
2.59-2.650.29121250.24932568X-RAY DIFFRACTION99.7
2.65-2.720.27881450.24792561X-RAY DIFFRACTION99.82
2.72-2.790.28431130.242619X-RAY DIFFRACTION99.78
2.79-2.880.25741330.2392582X-RAY DIFFRACTION99.74
2.88-2.970.26821380.22692581X-RAY DIFFRACTION99.89
2.97-3.070.25451300.21972540X-RAY DIFFRACTION99.85
3.07-3.20.28291180.21132629X-RAY DIFFRACTION99.82
3.2-3.340.21911550.19382579X-RAY DIFFRACTION99.89
3.34-3.520.24531080.1782629X-RAY DIFFRACTION99.96
3.52-3.740.18941410.16792593X-RAY DIFFRACTION100
3.74-4.030.21211650.14082584X-RAY DIFFRACTION99.96
4.03-4.430.16051360.11862631X-RAY DIFFRACTION100
4.43-5.070.13411400.11642641X-RAY DIFFRACTION99.96
5.07-6.390.17521930.14522599X-RAY DIFFRACTION100
6.39-52.150.18641520.17622753X-RAY DIFFRACTION99.52
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)
13.775920166821.30918988842-3.065814368364.77531194775-0.2575987181737.131503687550.0599701159282-0.12391581763-0.0515183517307-0.2717696435990.133405825350.656252212590.233881906377-0.471835584922-0.1054312775410.246294533666-0.0186648447408-0.03354253587690.5574894316820.07050197230660.4915914834226.7518435214-12.590585695347.9357489541
20.9806257793420.385523338033-0.2114924890271.43530246184-0.5334274591810.9941614104570.0241387429245-0.0646587221560.03426933206130.05695136509120.08979003779630.3273211915020.135664522338-0.411758757954-0.1044437131470.319563832645-0.0500534034338-0.001180195724540.454444246670.03018201104330.33993813854338.3501208886-15.394687657751.4345813866
30.819608733213-0.0735729258296-0.1541893192381.6464435537-0.02784526184821.293874365420.01491707655530.0156763183221-0.0439561370794-0.0948276467914-0.0616262469106-0.2129570171330.2176985331490.1396277943360.05001979347350.2915866008810.009742794017210.005754367966870.3160707021520.02455941524240.27633033265165.6800199238-17.446217875746.3785177248
41.344109551580.08992289609920.01882005405611.86926250232-0.2363146834921.186099870650.03114634503690.0144745192982-0.254381215378-0.152093104955-0.01412346614960.0629108911070.630263096756-0.120220145844-0.01619921449090.594034286981-0.0739009726118-0.01854691323010.3425050584080.04245067867450.30898275473152.8422136613-42.171893081953.6896987271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:26)
2X-RAY DIFFRACTION2(chain A and resseq 27:213)
3X-RAY DIFFRACTION3(chain A and resseq 214:443)
4X-RAY DIFFRACTION4(chain A and resseq 444:636)

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