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- PDB-8j3m: Structure of GH1 Br2 beta-glucosidase from bovine rumen metagenome -

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Basic information

Entry
Database: PDB / ID: 8j3m
TitleStructure of GH1 Br2 beta-glucosidase from bovine rumen metagenome
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Glycoside hydrolase / GH1 / metagenome / beta-glucosidase
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsKaenying, W. / Kongsaeree, P.T. / Tagami, T.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other governmentNRCT5-RSA63002-09 Thailand
CitationJournal: Heliyon / Year: 2023
Title: Structural and mutational analysis of glycoside hydrolase family 1 Br2 beta-glucosidase derived from bovine rumen metagenome.
Authors: Kaenying, W. / Tagami, T. / Suwan, E. / Pitsanuwong, C. / Chomngam, S. / Okuyama, M. / Kongsaeree, P. / Kimura, A. / Kongsaeree, P.T.
History
DepositionApr 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,68418
Polymers212,3554
Non-polymers1,32914
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-153 kcal/mol
Surface area59810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.701, 113.873, 181.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-glucosidase /


Mass: 53088.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: bovine rumen metagenome
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: BG / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1S5SJM8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M sodium acetate trihydrate pH 7.4, 1.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.999→48.26 Å / Num. obs: 135781 / % possible obs: 91.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 45.447 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.083 / Rsym value: 0.073 / Net I/σ(I): 12.03
Reflection shellResolution: 1.999→2.12 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 23046 / CC1/2: 0.645 / Rrim(I) all: 0.821 / Rsym value: 0.725 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→48.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.204 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2651 1979 1.477 %
Rwork0.2329 130465 -
obs-133972 90.33 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.384 Å2-0 Å20 Å2
2--0.374 Å2-0 Å2
3----0.758 Å2
Refinement stepCycle: LAST / Resolution: 1.999→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14482 0 74 132 14688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01214970
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613572
X-RAY DIFFRACTIONr_angle_refined_deg0.9651.64320306
X-RAY DIFFRACTIONr_angle_other_deg0.3491.57431262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51651788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.035566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.008102406
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.54910752
X-RAY DIFFRACTIONr_chiral_restr0.0480.22076
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023668
X-RAY DIFFRACTIONr_nbd_refined0.2130.23161
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.213104
X-RAY DIFFRACTIONr_nbtor_refined0.1870.27540
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.27277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2469
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0870.26
X-RAY DIFFRACTIONr_nbd_other0.160.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.22
X-RAY DIFFRACTIONr_mcbond_it2.0444.1997164
X-RAY DIFFRACTIONr_mcbond_other2.0444.1997164
X-RAY DIFFRACTIONr_mcangle_it3.067.5448948
X-RAY DIFFRACTIONr_mcangle_other3.067.5458949
X-RAY DIFFRACTIONr_scbond_it2.1824.3987806
X-RAY DIFFRACTIONr_scbond_other2.1624.3817767
X-RAY DIFFRACTIONr_scangle_it3.4517.98811358
X-RAY DIFFRACTIONr_scangle_other3.4357.95911299
X-RAY DIFFRACTIONr_lrange_it4.72339.3817377
X-RAY DIFFRACTIONr_lrange_other4.72339.38617368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.0510.3721570.33710176X-RAY DIFFRACTION95.5079
2.051-2.1070.3351510.31710290X-RAY DIFFRACTION98.2867
2.107-2.1680.3411470.30910010X-RAY DIFFRACTION98.5638
2.168-2.2340.569820.5425211X-RAY DIFFRACTION52.8296
2.234-2.3070.604720.5514577X-RAY DIFFRACTION47.9377
2.307-2.3880.291260.2759083X-RAY DIFFRACTION97.8432
2.388-2.4780.3731300.2838729X-RAY DIFFRACTION97.4909
2.478-2.5790.2981270.2668399X-RAY DIFFRACTION97.351
2.579-2.6930.2991150.2498034X-RAY DIFFRACTION97.0581
2.693-2.8240.3061240.2557674X-RAY DIFFRACTION96.8094
2.824-2.9770.2771140.2477243X-RAY DIFFRACTION96.2202
2.977-3.1560.278980.2446876X-RAY DIFFRACTION95.8757
3.156-3.3730.283940.2366438X-RAY DIFFRACTION95.3298
3.373-3.6420.247910.2495818X-RAY DIFFRACTION92.4871
3.642-3.9870.26650.1984289X-RAY DIFFRACTION73.7966
3.987-4.4540.197780.1584938X-RAY DIFFRACTION93.6695
4.454-5.1360.157580.1474354X-RAY DIFFRACTION92.767
5.136-6.2730.221510.1793730X-RAY DIFFRACTION92.8536
6.273-8.7970.218460.1682923X-RAY DIFFRACTION92.4059
8.797-48.2570.181250.1751673X-RAY DIFFRACTION88.6221

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