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- PDB-4zoe: Crystal Structure of beta-glucosidase from Listeria innocua -

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Basic information

Entry
Database: PDB / ID: 4zoe
TitleCrystal Structure of beta-glucosidase from Listeria innocua
ComponentsLin1840 protein
KeywordsHYDROLASE / TIM barrel / beta-1 / 2-glucan degradation / cytosol
Function / homology
Function and homology information


beta-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 3 C-terminal domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily ...Glycoside hydrolase family 3 C-terminal domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria innocua serovar 6a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsNakajima, M. / Yoshida, R. / Miyanaga, A. / Abe, K. / Takahashi, Y. / Sugimoto, N. / Toyoizumi, H. / Nakai, H. / Kitaoka, M. / Taguchi, H.
CitationJournal: Plos One / Year: 2016
Title: Functional and Structural Analysis of a beta-Glucosidase Involved in beta-1,2-Glucan Metabolism in Listeria innocua
Authors: Nakajima, M. / Yoshida, R. / Miyanaga, A. / Abe, K. / Takahashi, Y. / Sugimoto, N. / Toyoizumi, H. / Nakai, H. / Kitaoka, M. / Taguchi, H.
History
DepositionMay 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin1840 protein
B: Lin1840 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4656
Polymers161,2322
Non-polymers2334
Water21,1321173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-28 kcal/mol
Surface area47780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.750, 95.100, 214.996
Angle α, β, γ (deg.)90.000, 96.340, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-1468-

HOH

21B-1453-

HOH

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Components

#1: Protein Lin1840 protein / Beta-glucosidase


Mass: 80616.039 Da / Num. of mol.: 2 / Mutation: K2E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain CLIP 11262) (bacteria)
Strain: CLIP 11262 / Gene: lin1840 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92AS9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1173 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, NaCl, LiSO4, glycerol

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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: Nov 20, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→28.38 Å / Num. obs: 163230 / % possible obs: 98.5 % / Redundancy: 4.9 % / Net I/σ(I): 8.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EX1

1ex1


Resolution: 1.8→28.17 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.045 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 8215 5 %RANDOM
Rwork0.1801 ---
obs0.183 154994 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.22 Å2 / Biso mean: 14.86 Å2 / Biso min: 2.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11190 0 26 1173 12389
Biso mean--13.53 21.18 -
Num. residues----1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01911423
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210925
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.97615475
X-RAY DIFFRACTIONr_angle_other_deg2.042325220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74951448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05125.447514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.732151989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8571550
X-RAY DIFFRACTIONr_chiral_restr0.1260.21759
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112994
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022432
X-RAY DIFFRACTIONr_rigid_bond_restr4.595322346
X-RAY DIFFRACTIONr_sphericity_free18.1235349
X-RAY DIFFRACTIONr_sphericity_bonded5.574522973
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 619 -
Rwork0.25 11053 -
all-11672 -
obs--95.82 %

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