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- PDB-4i8d: Crystal Structure of Beta-D-glucoside glucohydrolase from Trichod... -

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Basic information

Entry
Database: PDB / ID: 4i8d
TitleCrystal Structure of Beta-D-glucoside glucohydrolase from Trichoderma reesei
ComponentsBeta-D-glucoside glucohydrolase
KeywordsHYDROLASE / beta-glucosidase / Glycoside hydrolase family 3 / GH3 / cellobiose / glucose / n-glycosylation / Structural Genomics / PSI-Biology / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / polysaccharide catabolic process / extracellular region
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, 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 C-terminal domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / 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
beta-D-glucopyranose / beta-glucosidase
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å
AuthorsHelmich, K.E. / Banerjee, G. / Bianchetti, C.M. / Gudmundsson, M. / Sandgren, M. / Walton, J.D. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Biochemical Characterization and Crystal Structures of a Fungal Family 3 beta-Glucosidase, Cel3A from Hypocrea jecorina.
Authors: Karkehabadi, S. / Helmich, K.E. / Kaper, T. / Hansson, H. / Mikkelsen, N.E. / Gudmundsson, M. / Piens, K. / Fujdala, M. / Banerjee, G. / Scott-Craig, J.S. / Walton, J.D. / Phillips, G.N. / Sandgren, M.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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-D-glucoside glucohydrolase
B: Beta-D-glucoside glucohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,0688
Polymers150,9442
Non-polymers4,1256
Water8,035446
1
A: Beta-D-glucoside glucohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2704
Polymers75,4721
Non-polymers1,7993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-D-glucoside glucohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7984
Polymers75,4721
Non-polymers2,3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.410, 107.860, 125.860
Angle α, β, γ (deg.)90.000, 115.590, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a monomer.

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Components

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Protein / Non-polymers , 2 types, 448 molecules AB

#1: Protein Beta-D-glucoside glucohydrolase


Mass: 75471.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: expressed with native and P. pastoris alpha-factor signal peptides
Source: (gene. exp.) Trichoderma reesei (fungus) / Gene: AAA18473, bgl1 / Production host: Pichia Pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q12715, beta-glucosidase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein solution (25mM sodium acetate, pH5.0) mixed in a 1:1 ratio with the well solution (4% 2-propanol, 0.1M BTP pH9.0, 20% MEPEG 5K) Cryoprotected with 4%2-propanol, 25% MEPEG 5K, 0.1M ...Details: Protein solution (25mM sodium acetate, pH5.0) mixed in a 1:1 ratio with the well solution (4% 2-propanol, 0.1M BTP pH9.0, 20% MEPEG 5K) Cryoprotected with 4%2-propanol, 25% MEPEG 5K, 0.1M BTP pH9.0, 10% ethylene glycol, Vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 10.21 / Number: 229956 / Rmerge(I) obs: 0.147 / Χ2: 1.22 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 54914 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785099.510.0450.9494.1
5.386.7899.610.0720.9584.2
4.75.3899.410.0881.1514.2
4.274.798.810.0931.0614.1
3.974.2799.410.1021.1614.1
3.733.9799.710.1161.1514.2
3.553.7399.810.1331.2514.2
3.393.5599.910.1571.2434.2
3.263.3910010.1841.2184.3
3.153.2699.910.221.2914.2
3.053.1510010.2481.3614.2
2.963.0510010.2881.354.2
2.892.9699.910.3571.3144.2
2.822.8999.910.3931.3144.2
2.752.8210010.4661.2734.2
2.692.7510010.4831.2414.2
2.642.6910010.571.334.2
2.592.6410010.691.2224.2
2.542.5910010.7371.2264.2
2.52.5499.910.8491.2464.2
ReflectionResolution: 2.48→50 Å / Num. obs: 54914 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.147 / Χ2: 1.216 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.48-2.544.20.84927201.246199.9
2.54-2.594.20.73727651.2261100
2.59-2.644.20.6927261.2221100
2.64-2.694.20.5727181.331100
2.69-2.754.20.48327621.2411100
2.75-2.824.20.46627271.2731100
2.82-2.894.20.39327281.314199.9
2.89-2.964.20.35727431.314199.9
2.96-3.054.20.28827571.351100
3.05-3.154.20.24827531.3611100
3.15-3.264.20.2227571.291199.9
3.26-3.394.30.18427361.2181100
3.39-3.554.20.15727321.243199.9
3.55-3.734.20.13327491.251199.8
3.73-3.974.20.11627171.151199.7
3.97-4.274.10.10227591.161199.4
4.27-4.74.10.09327431.061198.8
4.7-5.384.20.08827271.151199.4
5.38-6.784.20.07227750.958199.6
6.78-504.10.04528200.949199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å44.89 Å
Translation2.5 Å44.89 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X40

2x40


Resolution: 2.48→44.89 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 20.831 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.914 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 1820 3.6 %RANDOM
Rwork0.2014 ---
obs0.2038 51066 91.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.17 Å2 / Biso mean: 48.4193 Å2 / Biso min: 18.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å21.07 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.48→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10621 0 276 446 11343
LS refinement shellResolution: 2.481→2.546 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 82 -
Rwork0.273 2667 -
all-2749 -
obs--67.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77810.35670.07590.18780.08750.30830.03810.1969-0.13770.01910.0697-0.05310.0053-0.0206-0.10780.1923-0.0338-0.15910.0775-0.01360.227738.077-0.17717.423
20.3880.10250.2650.2028-0.01260.2994-0.06550.0942-0.0160.01940.0499-0.0104-0.03620.05050.01560.1946-0.0325-0.17320.02930.0170.208871.39923.47239.057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:713 OR RESID 801:810 ) )A3 - 713
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:713 OR RESID 801:810 ) )A801 - 810
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 0:713 OR RESID 801:813 ) )B0 - 713
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 0:713 OR RESID 801:813 ) )B801 - 813

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