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- PDB-5z06: Crystal structure of beta-1,2-glucanase from Parabacteroides dist... -

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Basic information

Entry
Database: PDB / ID: 5z06
TitleCrystal structure of beta-1,2-glucanase from Parabacteroides distasonis
ComponentsBDI_3064 protein
KeywordsHYDROLASE / Sophorose / Parabacteroides / GH144 / Glycoside hydrolase / beta-1 / 2-glucanase / 2-glucan / 2-glucooligosaccharide
Function / homologyexo beta-1,2-glucooligosaccharide sophorohydrolase (non-reducing end) / Glycoamylase-like, conserved domain / Putative glucoamylase / hydrolase activity, acting on glycosyl bonds / periplasmic space / Immunoglobulin-like fold / Exo beta-1,2-glucooligosaccharide sophorohydrolase (non-reducing end)
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShimizu, H. / Nakajima, M. / Miyanaga, A. / Takahashi, Y. / Tanaka, N. / Kobayashi, K. / Sugimoto, N. / Nakai, H. / Taguchi, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Mishima Kaiun Memorial Foundation Japan
CitationJournal: Biochemistry / Year: 2018
Title: Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on beta-1,2-Glucooligosaccharides from Parabacteroides distasonis
Authors: Shimizu, H. / Nakajima, M. / Miyanaga, A. / Takahashi, Y. / Tanaka, N. / Kobayashi, K. / Sugimoto, N. / Nakai, H. / Taguchi, H.
History
DepositionDec 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 22, 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: BDI_3064 protein
B: BDI_3064 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,89114
Polymers163,8892
Non-polymers1,00112
Water9,476526
1
A: BDI_3064 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5378
Polymers81,9451
Non-polymers5937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area24110 Å2
MethodPISA
2
B: BDI_3064 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3536
Polymers81,9451
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.080, 123.337, 101.376
Angle α, β, γ (deg.)90.00, 107.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BDI_3064 protein


Mass: 81944.727 Da / Num. of mol.: 2 / Fragment: UNP residues 19-721
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: ATCC 8503 / Gene: BDI_3064 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6LGF6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200mM calcium acetate, 100mM imidazole/ hydrochloric acid pH 8.0, and 20%(w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.73 Å / Num. obs: 86780 / % possible obs: 97.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4410 / CC1/2: 0.739 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
BUCCANEERmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QT9

4qt9


Resolution: 2.1→46.73 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.195 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.224 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21936 4328 5 %RANDOM
Rwork0.17763 ---
obs0.17966 82451 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11325 0 62 526 11913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211728
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210258
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.93415922
X-RAY DIFFRACTIONr_angle_other_deg0.948323817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05951393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07323.98598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.965151835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0841562
X-RAY DIFFRACTIONr_chiral_restr0.0840.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113167
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022607
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7133.2575581
X-RAY DIFFRACTIONr_mcbond_other1.7133.2565580
X-RAY DIFFRACTIONr_mcangle_it2.5084.8796971
X-RAY DIFFRACTIONr_mcangle_other2.5074.886972
X-RAY DIFFRACTIONr_scbond_it2.0383.4366144
X-RAY DIFFRACTIONr_scbond_other2.0373.4366144
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1685.0818949
X-RAY DIFFRACTIONr_long_range_B_refined4.2538.13714827
X-RAY DIFFRACTIONr_long_range_B_other4.2538.13614827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 294 -
Rwork0.282 5905 -
obs--94.84 %

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