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- PDB-2e3z: Crystal structure of intracellular family 1 beta-glucosidase BGL1... -

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Basic information

Entry
Database: PDB / ID: 2e3z
TitleCrystal structure of intracellular family 1 beta-glucosidase BGL1A from the basidiomycete Phanerochaete chrysosporium in substrate-free form
ComponentsBeta-glucosidase
KeywordsHYDROLASE / TIM BARREL / GLYCOSIDE HYDROLASE FAMILY 1 / CLAN GH-A / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


cellobiose glucosidase activity / beta-glucosidase / beta-glucosidase activity / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNijikken, Y. / Tsukada, T. / Igarashi, K. / Samejima, M. / Fushinobu, S.
Citation
Journal: Febs Lett. / Year: 2007
Title: Crystal structure of intracellular family 1 beta-glucosidase BGL1A from the basidiomycete Phanerochaete chrysosporium
Authors: Nijikken, Y. / Tsukada, T. / Igarashi, K. / Samejima, M. / Wakagi, T. / Shoun, H. / Fushinobu, S.
#1: Journal: Appl.Microbiol.Biotechnol. / Year: 2006
Title: Molecular cloning and characterization of two intracellular beta-glucosidases belonging to glycoside hydrolase family 1 from the basidiomycete Phanerochaete chrysosporium
Authors: Tsukada, T. / Igarashi, K. / Yoshida, M. / Samejima, M.
History
DepositionDec 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)105,9182
Polymers105,9182
Non-polymers00
Water24,4461357
1
A: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)52,9591
Polymers52,9591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)52,9591
Polymers52,9591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.760, 121.970, 134.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer. The asymmetric unit contains two almost identical monomers.

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Components

#1: Protein Beta-glucosidase


Mass: 52959.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: bgl1A / Plasmid: pBAD/TOPO ThioFusion / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q25BW5, beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1357 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 15% PEG 6000, 12% isopropanol, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 210 / Detector: CCD / Date: Feb 15, 2005
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 173769 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 29.6
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.56 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBG

1cbg


Resolution: 1.5→37.25 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2303338.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.181 8458 4.9 %RANDOM
Rwork0.166 ---
all0.167 173202 --
obs0.166 172336 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.058 Å2 / ksol: 0.357448 e/Å3
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2--3.6 Å20 Å2
3----2.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.5→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7431 0 0 1357 8788
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.672.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 1367 4.8 %
Rwork0.2 26901 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis_peptide.param

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