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- PDB-5cg0: Crystal structure of Spodoptera frugiperda Beta-glycosidase -

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Basic information

Entry
Database: PDB / ID: 5cg0
TitleCrystal structure of Spodoptera frugiperda Beta-glycosidase
ComponentsBeta-glucosidase
KeywordsHYDROLASE / GH1 Glycosil-hydrolase / Spodoptera frugiperda Beta-glycosidase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
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 speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsTamaki, F.K. / Souza, D.P. / Souza, V.P. / Farah, S.C. / Marana, S.R.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)08/55914-9 Brazil
Sao Paulo Research Foundation (FAPESP)14/19439-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)08/57908-1 Brazil
Instituto Nacional de Ciencias e Tecnologia para o Bioetanol574002/2008-1 Brazil
CitationJournal: PLoS ONE / Year: 2016
Title: Using the Amino Acid Network to Modulate the Hydrolytic Activity of beta-Glycosidases.
Authors: Tamaki, F.K. / Souza, D.P. / Souza, V.P. / Ikegami, C.M. / Farah, C.S. / Marana, S.R.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,74118
Polymers337,0716
Non-polymers2,67012
Water23,7441318
1
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4506
Polymers112,3572
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint2 kcal/mol
Surface area34800 Å2
MethodPISA
2
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2476
Polymers112,3572
Non-polymers8904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint2 kcal/mol
Surface area34750 Å2
MethodPISA
3
E: Beta-glucosidase
F: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0446
Polymers112,3572
Non-polymers6874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-3 kcal/mol
Surface area33530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.825, 64.994, 257.189
Angle α, β, γ (deg.)93.160, 92.040, 112.180
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-glucosidase /


Mass: 56178.477 Da / Num. of mol.: 6 / Mutation: L325F, I326F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Plasmid: pPIC9 / Production host: Komagataella pastoris (fungus) / References: UniProt: O61594
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1318 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100 mM Bis-Tris-HCl, 100 mM NaCL, 22% (w/v) PEG 3350
PH range: 6.1 - 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2014
RadiationMonochromator: RIGAKU VARIMAX HF OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 173155 / % possible obs: 91.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.05 / Rrim(I) all: 0.095 / Χ2: 1 / Net I/av σ(I): 12.451 / Net I/σ(I): 12.1 / Num. measured all: 566584
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.183.20.539170760.7090.3560.65190
2.18-2.263.20.415168450.7940.2760.5021.00189.3
2.26-2.373.20.337166810.8730.2240.407188.1
2.37-2.493.10.261165300.9120.1740.316187.3
2.49-2.653.10.201164280.9490.1340.2431.00286.9
2.65-2.853.10.151166600.970.10.182187.6
2.85-3.143.10.104173630.9850.0690.125191.9
3.14-3.593.20.071182720.9930.0460.085196.3
3.59-4.523.70.053185690.9960.0320.062198
4.52-603.90.052187310.9960.0310.061199

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
d*TREKdata scaling
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VIF

3vif


Resolution: 2.09→49.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.707 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 8675 5 %RANDOM
Rwork0.1924 ---
obs0.1952 164477 90.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.35 Å2 / Biso mean: 42.899 Å2 / Biso min: 18.27 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.09→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23565 0 174 1318 25057
Biso mean--74.88 44.2 -
Num. residues----2906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01924536
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221946
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.94233384
X-RAY DIFFRACTIONr_angle_other_deg0.826350481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99752923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20323.8811278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86153804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.65415153
X-RAY DIFFRACTIONr_chiral_restr0.0970.23429
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026028
X-RAY DIFFRACTIONr_mcbond_it2.0734.12811662
X-RAY DIFFRACTIONr_mcbond_other2.0724.12611655
X-RAY DIFFRACTIONr_mcangle_it3.2756.18114570
LS refinement shellResolution: 2.091→2.145 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 592 -
Rwork0.344 11359 -
all-11951 -
obs--84.86 %

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