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- PDB-5dt5: Crystal structure of the GH1 beta-glucosidase from Exiguobacteriu... -

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Basic information

Entry
Database: PDB / ID: 5dt5
TitleCrystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in space group P21
ComponentsBeta-glucosidase
KeywordsHYDROLASE / GH1 family / beta-glucosidase / cold-active / tetramer
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
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
Biological speciesExiguobacterium antarcticum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å
AuthorsZanphorlin, L.M. / Giuseppe, P.O. / Tonoli, C.C.C. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/13309-0 Brazil
Sao Paulo Research Foundation (FAPESP)14/07135-1 Brazil
CitationJournal: Sci Rep / Year: 2016
Title: Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7.
Authors: Zanphorlin, L.M. / de Giuseppe, P.O. / Honorato, R.V. / Tonoli, C.C. / Fattori, J. / Crespim, E. / de Oliveira, P.S. / Ruller, R. / Murakami, M.T.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Beta-glucosidase
D: Beta-glucosidase
E: Beta-glucosidase
F: Beta-glucosidase
G: Beta-glucosidase
H: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,42313
Polymers431,9438
Non-polymers4805
Water2,288127
1
A: Beta-glucosidase
B: Beta-glucosidase
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,2607
Polymers215,9724
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-60 kcal/mol
Surface area59950 Å2
2
E: Beta-glucosidase
F: Beta-glucosidase
G: Beta-glucosidase
H: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,1646
Polymers215,9724
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-48 kcal/mol
Surface area59190 Å2
3
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0823
Polymers107,9862
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-21 kcal/mol
Surface area31360 Å2
MethodPISA
4
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1784
Polymers107,9862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-32 kcal/mol
Surface area31330 Å2
MethodPISA
5
E: Beta-glucosidase
F: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0823
Polymers107,9862
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-21 kcal/mol
Surface area30850 Å2
MethodPISA
6
G: Beta-glucosidase
H: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0823
Polymers107,9862
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-21 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.073, 104.599, 199.186
Angle α, β, γ (deg.)90.000, 105.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-glucosidase /


Mass: 53992.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium antarcticum (strain B7) (bacteria)
Strain: B7 / Gene: bglA, Eab7_0297 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: K0A8J9, beta-glucosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS (pH 8.5), 2% (v/v) PEG400 and 1.45 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.722
11-H, -K, H+L20.278
ReflectionResolution: 2.24→49.11 Å / Num. obs: 203452 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.54

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PTV

4ptv


Resolution: 2.24→49.11 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2203 / WRfactor Rwork: 0.2005 / FOM work R set: 0.8185 / SU B: 10.96 / SU ML: 0.135 / SU R Cruickshank DPI: 0.0635 / SU Rfree: 0.0435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 9851 4.9 %RANDOM
Rwork0.2094 ---
obs0.2103 190890 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.01 Å2 / Biso mean: 44.132 Å2 / Biso min: 18.05 Å2
Baniso -1Baniso -2Baniso -3
1-13.02 Å20 Å213.94 Å2
2---1.45 Å2-0 Å2
3----11.57 Å2
Refinement stepCycle: final / Resolution: 2.24→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28766 0 25 127 28918
Biso mean--62.26 35.48 -
Num. residues----3532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01929718
X-RAY DIFFRACTIONr_bond_other_d0.0060.0226244
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.90740404
X-RAY DIFFRACTIONr_angle_other_deg0.889360292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09153524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14524.1381624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.967154494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.76615128
X-RAY DIFFRACTIONr_chiral_restr0.0640.24077
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0234384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027712
X-RAY DIFFRACTIONr_mcbond_it0.8184.40214120
X-RAY DIFFRACTIONr_mcbond_other0.8184.40214119
X-RAY DIFFRACTIONr_mcangle_it1.4366.617636
LS refinement shellResolution: 2.238→2.296 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 433 -
Rwork0.366 7638 -
all-8071 -
obs--52.8 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1172.2362-111.7823244.6903
2160.8726-57.6947245.575
3193.0883-90.5491208.391
4139.0381-77.4722209.7938
5188.1263-75.033284.1263
6161.7451-60.2117330.0865
7145.4187-93.8108285.0013
8173.2727-105.8533331.4818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 445
2X-RAY DIFFRACTION2B1 - 441
3X-RAY DIFFRACTION3C3 - 445
4X-RAY DIFFRACTION4D3 - 445
5X-RAY DIFFRACTION5E3 - 440
6X-RAY DIFFRACTION6F3 - 441
7X-RAY DIFFRACTION7G1 - 441
8X-RAY DIFFRACTION8H3 - 445

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