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- PDB-1ghs: THE THREE-DIMENSIONAL STRUCTURES OF TWO PLANT BETA-GLUCAN ENDOHYD... -

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Basic information

Entry
Database: PDB / ID: 1ghs
TitleTHE THREE-DIMENSIONAL STRUCTURES OF TWO PLANT BETA-GLUCAN ENDOHYDROLASES WITH DISTINCT SUBSTRATE SPECIFICITIES
Components1,3-BETA-GLUCANASE
KeywordsHYDROLASE
Function / homology
Function and homology information


(1->3)-beta-D-glucan catabolic process / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / defense response to fungus
Similarity search - Function
Glycosyl hydrolases family 17 signature. / Glycoside hydrolase family 17, plant / Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glucan endo-1,3-beta-glucosidase GII
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsGarrett, T.P.J. / Varghese, J.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities.
Authors: Varghese, J.N. / Garrett, T.P. / Colman, P.M. / Chen, L. / Hoj, P.B. / Fincher, G.B.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of (1,3)-and (1,3;1,4)-Beta--D-Glucanases from Germinating Barley
Authors: Chen, L. / Garrett, T.P.J. / Varghese, J.N. / Fincher, G.B. / Hoj, P.B.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Evolution of Polysaccharide Hydrolase Substrate Specificity
Authors: Chen, L. / Fincher, G.B. / Hoj, P.J.
History
DepositionOct 12, 1993Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,3-BETA-GLUCANASE
B: 1,3-BETA-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)64,7542
Polymers64,7542
Non-polymers00
Water1,06359
1
A: 1,3-BETA-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)32,3771
Polymers32,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,3-BETA-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)32,3771
Polymers32,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.900, 86.900, 156.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO A 82 / 2: CIS PROLINE - PRO A 138
3: PHE A 274 - ALA A 275 OMEGA = 0.24 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CIS PROLINE - PRO B 82 / 5: CIS PROLINE - PRO B 138
6: PHE B 274 - ALA B 275 OMEGA = 0.07 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4929, 0.8692, -0.0394), (-0.8698, 0.4909, -0.0503), (-0.0243, 0.0591, 0.998)
Vector: 35.187, 44.84, 40.354)

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Components

#1: Protein 1,3-BETA-GLUCANASE


Mass: 32377.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley)
References: UniProt: P15737, glucan endo-1,3-beta-D-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
215 %satammonium sulfate1drop
3100 mMTris-HCl1drop
435 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 32509 / % possible obs: 78.4 % / Num. measured all: 114164 / Rmerge(I) obs: 0.098

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→6 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.179 -
obs0.179 22811
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4568 0 0 59 4627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.68

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