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- PDB-3w53: Crystal structure of psychrophilic beta-glucosidase BglU from Mic... -

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Basic information

Entry
Database: PDB / ID: 3w53
TitleCrystal structure of psychrophilic beta-glucosidase BglU from Micrococcus antarcticus
ComponentsBeta-glucosidase
KeywordsHYDROLASE / TIM barrel / beta-glucosidase
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 hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesMicrococcus antarcticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHou, Y.J. / Miao, L.L. / Li, D.F. / Liu, Z.P.
CitationJournal: To be Published
Title: Structural and biochemical identification of key factors responsible for cold adaptation of Micrococcus antarcticus beta-glucosidase BglU
Authors: Miao, L.L. / Hou, Y.J. / Fan, H.X. / Qu, J. / Qi, C. / Liu, Y. / Li, D.F. / Liu, Z.P.
History
DepositionJan 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)56,4292
Polymers56,3061
Non-polymers1221
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.280, 84.670, 184.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta-glucosidase


Mass: 56306.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus antarcticus (bacteria) / Gene: BglU / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B9V8P5, beta-glucosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2(mol/L) MgCl2, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 27, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→61.55 Å / Num. all: 23296 / Num. obs: 22807 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 32.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 14.2 / Num. unique all: 2905 / Rsym value: 0.073 / % possible all: 87.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z1S

2z1s


Resolution: 2.2→47.443 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.873 / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.38 / σ(I): 0 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1087 4.77 %RANDOM
Rwork0.1613 ---
all0.1613 23296 --
obs0.1632 22765 97.86 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.46 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 60.05 Å2 / Biso mean: 12 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.1378 Å20 Å20 Å2
2--0.3333 Å2-0 Å2
3---0.8045 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 8 442 4156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073816
X-RAY DIFFRACTIONf_angle_d1.075210
X-RAY DIFFRACTIONf_chiral_restr0.074552
X-RAY DIFFRACTIONf_plane_restr0.004690
X-RAY DIFFRACTIONf_dihedral_angle_d12.9721364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30020.23221070.1692336244386
2.3002-2.42140.2361270.1662652277997
2.4214-2.57310.21851320.166627422874100
2.5731-2.77180.20871250.171527322857100
2.7718-3.05070.23591640.170427352899100
3.0507-3.4920.21441330.167127692902100
3.492-4.39910.16041440.135628052949100
4.3991-47.45420.16721550.165229073062100

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