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- PDB-5idi: Structure of beta glucosidase 1A from Thermotoga neapolitana, mut... -

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Basic information

Entry
Database: PDB / ID: 5idi
TitleStructure of beta glucosidase 1A from Thermotoga neapolitana, mutant E349A
Components1,4-beta-D-glucan glucohydrolase
KeywordsHYDROLASE / beta-glucosidase / glycosyl hydrolase family 1
Function / homology
Function and homology information


glucan 1,4-beta-glucosidase / glucan 1,4-beta-glucosidase activity / beta-glucosidase / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,4-beta-D-glucan glucohydrolase
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKulkarni, T. / Nordberg Karlsson, E. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Sweden
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of beta-glucosidase 1A from Thermotoga neapolitana and comparison of active site mutants for hydrolysis of flavonoid glucosides.
Authors: Kulkarni, T.S. / Khan, S. / Villagomez, R. / Mahmood, T. / Lindahl, S. / Logan, D.T. / Linares-Pasten, J.A. / Nordberg Karlsson, E.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,4-beta-D-glucan glucohydrolase
B: 1,4-beta-D-glucan glucohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4035
Polymers105,2262
Non-polymers1773
Water7,728429
1
A: 1,4-beta-D-glucan glucohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7313
Polymers52,6131
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,4-beta-D-glucan glucohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6722
Polymers52,6131
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.277, 98.726, 154.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1,4-beta-D-glucan glucohydrolase / Glucan glucohydrolase / Beta-D-glucoside glucohydrolase / Beta-glucosidase / Glucan 1 / 4-beta-glucosidase


Mass: 52613.117 Da / Num. of mol.: 2 / Mutation: E349G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Gene: gghA, CTN_0782 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B9K7M5, glucan 1,4-beta-glucosidase, beta-glucosidase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 5
Details: Protein at 12 mg/ml in 20 mM citrate phosphate buffer, pH 5.6. Hanging drops consisting of 1 microlitre of protein solution and 2 microlitres of reservoir solution (18-23% w/v PEG 6000, 0.2 ...Details: Protein at 12 mg/ml in 20 mM citrate phosphate buffer, pH 5.6. Hanging drops consisting of 1 microlitre of protein solution and 2 microlitres of reservoir solution (18-23% w/v PEG 6000, 0.2 M sodium chloride, 0.1 M sodium acetate, pH 5.0) equilibrated against 1 ml of reservoir solution. Rod-shaped crystals of approximate dimensions 0.3 x 0.2 x 0.3 mm grew after 8-10 days.
PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0402 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0402 Å / Relative weight: 1
ReflectionResolution: 1.9→30.1 Å / Num. obs: 81717 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.172 / Mean I/σ(I) obs: 1.9 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CBV

2cbv


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.008 / SU ML: 0.099 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 4096 5 %RANDOM
Rwork0.16857 ---
obs0.17082 77455 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.434 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---0.42 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7300 0 12 429 7741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0197542
X-RAY DIFFRACTIONr_bond_other_d0.0020.026932
X-RAY DIFFRACTIONr_angle_refined_deg2.241.92310237
X-RAY DIFFRACTIONr_angle_other_deg1.191315902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83123.769398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.176151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9851544
X-RAY DIFFRACTIONr_chiral_restr0.1550.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218624
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021920
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_it1.3131.6933551
X-RAY DIFFRACTIONr_mcbond_other1.2831.6913547
X-RAY DIFFRACTIONr_mcangle_it1.842.534432
X-RAY DIFFRACTIONr_mcangle_other1.842.5314433
X-RAY DIFFRACTIONr_scbond_it2.2021.9353991
X-RAY DIFFRACTIONr_scbond_other2.2021.9353992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4332.8055805
X-RAY DIFFRACTIONr_long_range_B_refined4.99214.3988935
X-RAY DIFFRACTIONr_long_range_B_other4.94714.1998821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.895→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 274 -
Rwork0.423 4949 -
obs--87.4 %
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)
10.6014-0.1077-0.14590.4837-0.04720.50030.0352-0.08340.04020.0303-0.0033-0.0522-0.0150.0834-0.03190.0851-0.02260.0230.0236-0.01250.0593-20.25-9.57332.378
20.79160.20990.05070.5267-0.00990.5257-0.05390.04570.0663-0.11320.02710.0256-0.0479-0.04930.02680.1418-0.00030.03530.00890.00650.048-50.6092.2592.411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 444
2X-RAY DIFFRACTION2A1 - 443

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