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

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Basic information

Entry
Database: PDB / ID: 1ghr
TitleTHE THREE-DIMENSIONAL STRUCTURES OF TWO PLANT BETA-GLUCAN ENDOHYDROLASES WITH DISTINCT SUBSTRATE SPECIFICITIES
Components1,3-1,4-BETA-GLUCANASE
KeywordsHYDROLASE
Function / homology
Function and homology information


licheninase / licheninase activity / carbohydrate metabolic process
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
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsVarghese, J.N. / Garrett, T.P.J.
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 11, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,3-1,4-BETA-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)32,1411
Polymers32,1411
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.400, 87.400, 109.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 137
2: PHE 275 - ALA 276 OMEGA = 11.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein 1,3-1,4-BETA-GLUCANASE


Mass: 32141.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / References: UniProt: P12257, licheninase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: GUB2_HORVU SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE PHE 30 SER 24

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMTris-HCl1drop
325 %satammonium sulfate1drop
445 %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: 16399 / % possible obs: 82 % / Num. measured all: 86286 / Rmerge(I) obs: 0.101

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.176 -
obs0.176 13568
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 0 141 2898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.62
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: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.62

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