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- PDB-2ayh: CRYSTAL AND MOLECULAR STRUCTURE AT 1.6 ANGSTROMS RESOLUTION OF TH... -

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Basic information

Entry
Database: PDB / ID: 2ayh
TitleCRYSTAL AND MOLECULAR STRUCTURE AT 1.6 ANGSTROMS RESOLUTION OF THE HYBRID BACILLUS ENDO-1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE H(A16-M)
Components1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
KeywordsHYDROLASE (GLUCANASE)
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Beta-glucanase/XTH / Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological specieshybrid (others)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsHahn, M. / Keitel, T. / Heinemann, U.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Crystal and molecular structure at 0.16-nm resolution of the hybrid Bacillus endo-1,3-1,4-beta-D-glucan 4-glucanohydrolase H(A16-M).
Authors: Hahn, M. / Keitel, T. / Heinemann, U.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Molecular and Active-Site Structure of a Bacillus 1,3-1,4-Beta-Glucanase
Authors: Keitel, T. / Simon, O. / Borriss, R. / Heinemann, U.
History
DepositionFeb 2, 1995Processing site: BNL
SupersessionMar 31, 1995ID: 1AYH
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9752
Polymers23,9351
Non-polymers401
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.180, 78.260, 39.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 201

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Components

#1: Protein 1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE


Mass: 23935.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) hybrid (others) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P23904, licheninase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND HYBRID PROTEIN MOLECULE; RESIDUES 1 - 16 ARE DERIVED FROM THE BACILLUS AMYLOLIQUEFACIENS ...COMPND HYBRID PROTEIN MOLECULE; RESIDUES 1 - 16 ARE DERIVED FROM THE BACILLUS AMYLOLIQUEFACIENS BETA-GLUCANASE AND RESIDUES 17 - 214 ARE DERIVED FROM THE HOMOLOGOUS BACILLUS MACERANS BETA-GLUCANASE. EXPRESSED IN ESCHERICHIA COLI, PLASMID PBR322.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
Conc.: 12-16 %(w/v) / Common name: PEG6000

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Data collection

Reflection
*PLUS
Num. obs: 21561 / % possible obs: 80.4 % / Observed criterion σ(I): 1 / Rmerge F obs: 0.109

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.6→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.143 21032
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 1 202 1904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.92
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.197 / Rfactor obs: 0.143 / Rfactor Rfree: 0.22 / Rfactor Rwork: 13.1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 2.92

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