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- PDB-3ahx: Crystal structure of beta-glucosidase A from bacterium Clostridiu... -

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Basic information

Entry
Database: PDB / ID: 3ahx
TitleCrystal structure of beta-glucosidase A from bacterium Clostridium cellulovorans
ComponentsBeta-glucosidase A
KeywordsHYDROLASE / cellulases / glycosyl hydrolase / manganese enhancement
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / 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
Chem-7PE / Beta-glucosidase
Similarity search - Component
Biological speciesClostridium cellulovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 A
B: Beta-glucosidase A
C: Beta-glucosidase A
D: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,4136
Polymers210,7924
Non-polymers6212
Water38,6782147
1
A: Beta-glucosidase A


Theoretical massNumber of molelcules
Total (without water)52,6981
Polymers52,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase A


Theoretical massNumber of molelcules
Total (without water)52,6981
Polymers52,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0082
Polymers52,6981
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0082
Polymers52,6981
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.498, 128.498, 264.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Beta-glucosidase A


Mass: 52698.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulovorans (bacteria) / Gene: BglA / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: Q53EH2, beta-glucosidase
#2: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2147 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 21-23%(w/v) PEG 3350, 0.3-0.45M Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2008
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 172709 / Num. obs: 171402 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.8 / Num. unique all: 17061 / % possible all: 98

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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 1OD0

1od0


Resolution: 1.9→28.3 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.954 / SU ML: 0.079 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 3.573 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19832 7980 5 %RANDOM
Rwork0.14606 ---
obs0.14867 151131 92.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.123 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2--1.69 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14530 0 42 2147 16719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214978
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.93620283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.69851768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03124.235791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.089152476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9781576
X-RAY DIFFRACTIONr_chiral_restr0.1050.22068
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111672
X-RAY DIFFRACTIONr_mcbond_it1.2591.58796
X-RAY DIFFRACTIONr_mcangle_it2.01214120
X-RAY DIFFRACTIONr_scbond_it3.11136182
X-RAY DIFFRACTIONr_scangle_it4.6354.56163
X-RAY DIFFRACTIONr_rigid_bond_restr2.042314978
X-RAY DIFFRACTIONr_sphericity_free6.29232208
X-RAY DIFFRACTIONr_sphericity_bonded3.303314572
LS refinement shellResolution: 1.902→2.005 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.233 1015 -
Rwork0.158 19522 -
obs--82.54 %
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)
10.37280.132-0.15680.6129-0.2010.5979-0.03130.0146-0.0017-0.06620.0361-0.0560.0527-0.0179-0.00480.0263-0.0265-0.00330.03130.00460.0383122.756942.9707-267.2584
20.3919-0.0934-0.17030.1903-0.06150.58010.0562-0.02510.0415-0.002-0.0252-0.019-0.11850.0503-0.03110.0577-0.01980.02290.0116-0.0040.0397104.71582.2706-283.1528
30.7265-0.0311-0.00060.38850.03820.28860.0942-0.0994-0.04740.0104-0.05890.02380.0074-0.0336-0.03530.0707-0.0693-0.00240.07610.00480.052479.830428.6937-262.4589
40.43290.24320.0370.812-0.05560.5060.05330.01710.0563-0.0347-0.07470.12980.0144-0.03060.02140.01330.0105-0.00290.0153-0.01450.041369.095357.2499-296.235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 444
2X-RAY DIFFRACTION2B1 - 444
3X-RAY DIFFRACTION3C4 - 444
4X-RAY DIFFRACTION4D2 - 444

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