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- PDB-1cbg: THE CRYSTAL STRUCTURE OF A CYANOGENIC BETA-GLUCOSIDASE FROM WHITE... -

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Basic information

Entry
Database: PDB / ID: 1cbg
TitleTHE CRYSTAL STRUCTURE OF A CYANOGENIC BETA-GLUCOSIDASE FROM WHITE CLOVER (TRIFOLIUM REPENS L.), A FAMILY 1 GLYCOSYL-HYDROLASE
ComponentsCYANOGENIC BETA-GLUCOSIDASE
KeywordsHYDROLASE (O-GLYCOSYL) / CYANOGENIC BETA-GLUCOSIDASE
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
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
Cyanogenic beta-glucosidase
Similarity search - Component
Biological speciesTrifolium repens (white clover)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsBarrett, T.E. / Suresh, C.G. / Tolley, S.P. / Hughes, M.A.
Citation
Journal: Structure / Year: 1995
Title: The crystal structure of a cyanogenic beta-glucosidase from white clover, a family 1 glycosyl hydrolase.
Authors: Barrett, T. / Suresh, C.G. / Tolley, S.P. / Dodson, E.J. / Hughes, M.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary Crystallographic Analysis of the Cyanogenic Beta-Glucosidase from the White Clover Trifolium Repens L
Authors: Tolley, S.P. / Barrett, T.E. / Suresh, C.G. / Hughes, M.A.
History
DepositionJul 31, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYANOGENIC BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)56,4201
Polymers56,4201
Non-polymers00
Water7,855436
1
A: CYANOGENIC BETA-GLUCOSIDASE

A: CYANOGENIC BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)112,8392
Polymers112,8392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2710 Å2
ΔGint-20 kcal/mol
Surface area37210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.326, 70.326, 249.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO 199
2: TRP 446 - SER 447 OMEGA = 358.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: PHE 1 .. LYS 490 THE CYANOGENIC BETA-GLUCOSIDASE FROM WHITE CLOVER EXISTS AS A HOMODIMER IN SOLUTION. THE DIMERS ARE RELATED BY THE CRYSTALLOGRAPHIC TWO-FOLD AXIS PASSING THROUGH THE UNIT CELL ORIGIN IN THE AB PLANE. SYMMETRY1 1 0.000000 -1.000000 0.000000 1.00000 SYMMETRY2 1 -1.000000 0.000000 0.000000 1.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 0.50000

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Components

#1: Protein CYANOGENIC BETA-GLUCOSIDASE


Mass: 56419.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trifolium repens (white clover) / Organ: LEAVES / Variant: L / Tissue: LEAVES / References: UniProt: P26205, beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop / Details: Tolley, S.P., (1993) J.Mol.Biol., 229, 791.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
148-52 %(w/v)ammonium sulphate1reservoir
2200 mMTris-maleate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.15→15 Å / Num. obs: 30663 / % possible obs: 88 % / Observed criterion σ(I): 3.5 / Redundancy: 3 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
DENZOdata reduction
ARP/wARPmodel building
X-PLOR3.1model building
PROLSQrefinement
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.15→9 Å / σ(F): 0
Details: WATER MOLECULES WITH OCCUPANCIES OF 0.5 HAVE BEEN ASSIGNED TO DENSITY THAT IS PROBABLY ATTRIBUTABLE TO GLYCOSYLATION (IN THE VICINITY OF RESIDUES ASN 15 AND ASN 315) BUT IS OF INSUFFICIENT ...Details: WATER MOLECULES WITH OCCUPANCIES OF 0.5 HAVE BEEN ASSIGNED TO DENSITY THAT IS PROBABLY ATTRIBUTABLE TO GLYCOSYLATION (IN THE VICINITY OF RESIDUES ASN 15 AND ASN 315) BUT IS OF INSUFFICIENT QUALITY TO MODEL AS SUGAR RESIDUES.
RfactorNum. reflection% reflection
Rfree0.247 -10 %
Rwork0.195 --
obs0.195 27250 95 %
Displacement parametersBiso mean: 12 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.15→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 0 436 4429
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.84
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.259
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.4351.5
X-RAY DIFFRACTIONx_mcangle_it0.7612
X-RAY DIFFRACTIONx_scbond_it0.8152
X-RAY DIFFRACTIONx_scangle_it1.2663
Refinement
*PLUS
Rfactor obs: 0.189 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.010.02
X-RAY DIFFRACTIONx_angle_d0.0360.04
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.84
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.259
X-RAY DIFFRACTIONx_planar_d0.0370.05
X-RAY DIFFRACTIONx_plane_restr0.0110.02
X-RAY DIFFRACTIONx_chiral_restr0.01020.12

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