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- PDB-1qox: Beta-glucosidase from Bacillus circulans sp. alkalophilus -

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Basic information

Entry
Database: PDB / ID: 1qox
TitleBeta-glucosidase from Bacillus circulans sp. alkalophilus
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / CELLULOSE DEGRADATION
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
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHakulinen, N. / Rouvinen, J.
CitationJournal: J.Struct.Biol. / Year: 2000
Title: The Crystal Structure of Beta-Glucosidase from Bacillus Circulans Sp. Alkalophilus: Ability to Form Long Polymeric Assemblies
Authors: Hakulinen, N. / Paavilainen, S. / Korpela, T. / Rouvinen, J.
History
DepositionNov 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN (E.G. SHEET AB IN CHAIN ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "B" IN EACH CHAIN (E.G. SHEET AB IN CHAIN A) ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
G: BETA-GLUCOSIDASE
H: BETA-GLUCOSIDASE
I: BETA-GLUCOSIDASE
J: BETA-GLUCOSIDASE
K: BETA-GLUCOSIDASE
L: BETA-GLUCOSIDASE
M: BETA-GLUCOSIDASE
N: BETA-GLUCOSIDASE
O: BETA-GLUCOSIDASE
P: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)819,56016
Polymers819,56016
Non-polymers00
Water44,1012448
1
A: BETA-GLUCOSIDASE
B: BETA-GLUCOSIDASE
C: BETA-GLUCOSIDASE
D: BETA-GLUCOSIDASE
E: BETA-GLUCOSIDASE
F: BETA-GLUCOSIDASE
G: BETA-GLUCOSIDASE
H: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)409,7808
Polymers409,7808
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
I: BETA-GLUCOSIDASE
J: BETA-GLUCOSIDASE
K: BETA-GLUCOSIDASE
L: BETA-GLUCOSIDASE
M: BETA-GLUCOSIDASE
N: BETA-GLUCOSIDASE
O: BETA-GLUCOSIDASE
P: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)409,7808
Polymers409,7808
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.400, 122.300, 163.200
Angle α, β, γ (deg.)89.30, 74.30, 68.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.005, -0.8308, 0.5565), (0.8437, 0.2952, 0.4483), (-0.5367, 0.4718, 0.6995)0.058, -0.033, 0.208
2given(-1, 0.0051, 0.0037), (0.0012, -0.4134, 0.91), (0.0061, 0.9105, 0.4134)0.203, 0.139, -0.162
3given(-0.0035, 0.8409, -0.5412), (-0.8391, 0.292, 0.459), (0.544, 0.4557, 0.7046)-0.189, 0.403, -0.328
4given(0.9833, -0.1594, 0.0875), (-0.16, -0.9871, 0.0006), (0.0863, -0.0146, -0.9962)-0.043, 0.084, -0.027
5given(-0.1802, -0.8211, 0.5416), (-0.8259, -0.1728, -0.5367), (0.5343, -0.544, -0.647)-0.031, 0.65, 0.138
6given(-0.9848, 0.1451, -0.0955), (0.147, 0.4033, -0.9032), (-0.0925, -0.9035, -0.4185)0.256, 0.088, 0.43
7given(0.1731, 0.8197, -0.546), (0.8236, -0.4245, -0.3761), (-0.5401, -0.3846, -0.7486)-0.119, 0.018, 0.244
8given(-0.6165, 0.6619, -0.4264), (-0.6493, -0.1211, 0.7508), (0.4453, 0.7398, 0.5045)0.849, 52.27, 80.28
9given(0.7953, 0.5122, -0.3242), (-0.5135, 0.8535, 0.0885), (0.3221, 0.0961, 0.9418)0.593, 52.062, 79.911
10given(0.6176, -0.6508, 0.4415), (0.6625, 0.7331, 0.154), (-0.4239, 0.1974, 0.8839)0.853, 51.716, 80.38
11given(-0.7901, -0.5076, 0.3437), (0.5175, -0.2516, 0.8179), (-0.3287, 0.824, 0.4615)1.266, 51.769, 80.355
12given(-0.7475, -0.56, 0.3574), (-0.5505, 0.2212, -0.805), (0.3717, -0.7985, -0.4736)0.933, 52.378, 80.6
13given(-0.6684, 0.6208, -0.4097), (0.6235, 0.1672, -0.7638), (-0.4056, -0.7659, -0.4988)0.99, 51.782, 80.794
14given(0.7454, 0.5512, -0.375), (0.5546, -0.8248, -0.1101), (-0.37, -0.1259, -0.92)0.609, 52.018, 80.535
15given(0.6691, -0.6298, 0.3945), (-0.6325, -0.7613, -0.1426), (0.3902, -0.1541, -0.9077)0.614, 52.221, 80.263

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Components

#1: Protein
BETA-GLUCOSIDASE /


Mass: 51222.477 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) BACILLUS CIRCULANS (bacteria) / Strain: ALKALOPHILUS / References: UniProt: Q03506, beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2448 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 6
Details: 13 % PEG8000, 0.3 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, PH 6.0
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
313 %PEG80001reservoir
40.3 Msodium formate1reservoir
50.1 Msodium acetate1reservoir
2Tris(tris(hydroxymethyl)aminomethane)1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 15, 1997
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→99 Å / Num. obs: 186165 / % possible obs: 83.7 % / Redundancy: 1.63 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.076 / Net I/σ(I): 8.7
Reflection shellResolution: 2.69→2.78 Å / Redundancy: 1.47 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.322 / % possible all: 66
Reflection
*PLUS
Num. measured all: 303163 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 66 % / Rmerge(I) obs: 0.322

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BGA

1bga


Resolution: 2.7→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.255 --
obs0.255 167801 84 %
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57856 0 0 2448 60304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.07
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.656
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.908
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.908

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