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- PDB-3ahy: Crystal structure of beta-glucosidase 2 from fungus Trichoderma r... -

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Basic information

Entry
Database: PDB / ID: 3ahy
TitleCrystal structure of beta-glucosidase 2 from fungus Trichoderma reesei in complex with Tris
ComponentsBeta-glucosidase
KeywordsHYDROLASE / cellulases / glycosyl hydrolase / manganese enhancement
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / 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 speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsJeng, W.-Y. / Liu, C.-I. / Wang, A.H.-J.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural and functional analysis of three beta-glucosidases from bacterium Clostridium cellulovorans, fungus Trichoderma reesei and termite Neotermes koshunensis
Authors: Jeng, W.-Y. / Wang, N.-C. / Lin, M.-H. / Lin, C.-T. / Liaw, Y.-C. / Chang, W.-J. / Liu, C.-I. / Liang, P.-H. / Wang, A.H.-J.
History
DepositionMay 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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)213,5188
Polymers213,0304
Non-polymers4894
Water55,8473100
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3802
Polymers53,2571
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3802
Polymers53,2571
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3802
Polymers53,2571
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3802
Polymers53,2571
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.830, 103.511, 94.802
Angle α, β, γ (deg.)90.00, 105.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-glucosidase


Mass: 53257.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei (fungus) / Gene: Bgl2 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: O93785, beta-glucosidase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3100 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 20-22%(w/v) PEG 3350, 0.23M MgCl2, 12.5mM sodium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2009 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. all: 217400 / Num. obs: 210766 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.9
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.5 / Num. unique all: 21633 / % possible all: 95.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E3Z

2e3z


Resolution: 1.63→29.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.315 / SU ML: 0.069 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21771 10155 5 %RANDOM
Rwork0.16441 ---
obs0.16704 192806 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.638 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.23 Å2
2---0.3 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.63→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14791 0 32 3100 17923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02215265
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9420751
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.70551857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26723.36762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.491152306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.72915108
X-RAY DIFFRACTIONr_chiral_restr0.1070.22109
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112108
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0181.59261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.553214861
X-RAY DIFFRACTIONr_scbond_it2.46936004
X-RAY DIFFRACTIONr_scangle_it3.5124.55890
X-RAY DIFFRACTIONr_rigid_bond_restr1.452315265
X-RAY DIFFRACTIONr_sphericity_free3.98633100
X-RAY DIFFRACTIONr_sphericity_bonded2.45314823
LS refinement shellResolution: 1.63→1.718 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.244 1434 -
Rwork0.169 26234 -
obs--88.54 %
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)
10.39090.0707-0.08180.2396-0.00110.2907-0.0004-0.0580.01360.02020.0081-0.0367-0.00170.0352-0.00770.0129-0.0018-0.00340.0259-0.00690.0074-5.356-80.150410.3734
20.2658-0.04960.01170.24830.01690.32420.02510.01190.0121-0.0114-0.0166-0.05230.00490.0458-0.00850.0150.00020.01010.01190.00190.01596.9214-82.5437-34.3065
30.2425-0.06650.06120.3613-0.05290.24820.0026-0.02240.0045-0.0229-0.00180.0439-0.0027-0.0158-0.00080.02050.00340.00390.0032-0.00060.0086-36.0967-66.1197-44.0217
40.80380.32770.09230.41330.02570.1924-0.01520.0355-0.0079-0.00940.02010.03750.00640.0094-0.00490.0135-0.0013-0.00010.00210.00040.006-46.2711-99.5514-2.3838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 465
2X-RAY DIFFRACTION2B0 - 465
3X-RAY DIFFRACTION3C0 - 464
4X-RAY DIFFRACTION4D1 - 465

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