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- PDB-5dt7: Crystal structure of the GH1 beta-glucosidase from Exiguobacteriu... -

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Basic information

Entry
Database: PDB / ID: 5dt7
TitleCrystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in space group C2221
ComponentsBeta-glucosidase
KeywordsHYDROLASE / GH1 family / beta-glucosidase / cold-active / tetramer
Function / homology
Function and homology information


: / 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 / Resolution: 2.15 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: pdbx_audit_support / pdbx_struct_oper_list
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,99020
Polymers215,9724
Non-polymers2,01816
Water9,350519
1
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules

A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,98620
Polymers215,9724
Non-polymers2,01416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
2
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules

C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,99420
Polymers215,9724
Non-polymers2,02216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
3
A: Beta-glucosidase
hetero molecules

A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,18112
Polymers107,9862
Non-polymers1,19510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area3860 Å2
ΔGint-65 kcal/mol
Surface area31450 Å2
MethodPISA
4
B: Beta-glucosidase
hetero molecules

B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8058
Polymers107,9862
Non-polymers8196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area2950 Å2
ΔGint-32 kcal/mol
Surface area31340 Å2
MethodPISA
5
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,99710
Polymers107,9862
Non-polymers1,0118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-56 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.975, 376.119, 109.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

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Components

#1: Protein
Beta-glucosidase


Mass: 53992.887 Da / Num. of mol.: 4
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-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M CAPS (pH 10.5), 0.2 M lithium sulfate and 2 M ammonium sulfate using in situ proteolysis (1:1000 (w/w) ratio of trypsin:protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 123301 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 42.751 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.103 / Χ2: 1.094 / Net I/σ(I): 8.19 / Num. measured all: 776096
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.15-2.280.6910.7561.179094640832391850.96596
2.28-2.430.8520.4521.9510433038382383260.56699.9
2.43-2.630.9310.2933.2611323335705356810.35499.9
2.63-2.880.970.1945.211418732925329050.22999.9
2.88-3.220.9870.128.3510100629751296900.14399.8
3.22-3.710.9930.07413.948656326236260610.08999.3
3.71-4.540.9960.05519.877628822173220140.06599.3
4.54-6.390.9950.0521.595778717201170900.05999.4
6.390.9970.04423.9731756959194130.05398.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PTV

4ptv


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12.892 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 6550 5 %RANDOM
Rwork0.1875 ---
obs0.189 123301 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.9 Å2 / Biso mean: 44.182 Å2 / Biso min: 27.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.62 Å20 Å2
3---1.42 Å2
Refinement stepCycle: final / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14456 0 121 519 15096
Biso mean--56.33 42.62 -
Num. residues----1776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915032
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213309
X-RAY DIFFRACTIONr_angle_refined_deg1.361.91420424
X-RAY DIFFRACTIONr_angle_other_deg0.955330594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56251772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30224.145813
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.921152265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0441564
X-RAY DIFFRACTIONr_chiral_restr0.0810.22067
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023871
X-RAY DIFFRACTIONr_mcbond_it1.5454.3357100
X-RAY DIFFRACTIONr_mcbond_other1.5454.3347099
X-RAY DIFFRACTIONr_mcangle_it2.346.4948868
LS refinement shellResolution: 2.147→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 487 -
Rwork0.364 8589 -
all-9076 -
obs--96.56 %
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)
131.2067170.747389.5681
254.022134.9038109.4138
336.046195.666673.4105
462.869949.185459.1253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 446
2X-RAY DIFFRACTION2B1 - 442
3X-RAY DIFFRACTION3C1 - 445
4X-RAY DIFFRACTION4D1 - 445

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