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- PDB-3cmj: Crystal Structure of engineered Beta-Glucosidase from Soil metagenome -

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Basic information

Entry
Database: PDB / ID: 3cmj
TitleCrystal Structure of engineered Beta-Glucosidase from Soil metagenome
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Bgl
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / 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
S,R MESO-TARTARIC ACID / Beta-glucosidase
Similarity search - Component
Biological speciesUncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsHwang, K.Y. / Nam, K.H.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of engineered beta-glucosidase from a soil metagenome.
Authors: Nam, K.H. / Kim, S.J. / Kim, M.Y. / Kim, J.H. / Yeo, Y.S. / Lee, C.M. / Jun, H.K. / Hwang, K.Y.
History
DepositionMar 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,25324
Polymers52,5971
Non-polymers65623
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.331, 71.002, 86.978
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: 52596.832 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: E39N, L40V, Q41K, P42K, K45E, R477N, A481E, A482D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Uncultured bacterium (environmental samples)
Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0GMU3, beta-glucosidase
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na/K tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23986 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23986 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 54735 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rsym value: 0.062 / Net I/σ(I): 35.57
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rsym value: 0.186

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementStarting model: PDB code 1OIM

1oim


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.349 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2756 5 %RANDOM
Rwork0.163 ---
obs0.165 54699 94.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 32 367 3930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223643
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9414955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8775440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09723.636187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9711527
X-RAY DIFFRACTIONr_chiral_restr0.1280.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022891
X-RAY DIFFRACTIONr_nbd_refined0.2110.21869
X-RAY DIFFRACTIONr_nbtor_refined0.310.22501
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2326
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.220
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0740.21
X-RAY DIFFRACTIONr_mcbond_it0.581.52191
X-RAY DIFFRACTIONr_mcangle_it1.11823510
X-RAY DIFFRACTIONr_scbond_it1.89531539
X-RAY DIFFRACTIONr_scangle_it3.1084.51445
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 140 -
Rwork0.201 2544 -
all-2684 -
obs--63.6 %

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