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- PDB-1glh: CATION BINDING TO A BACILLUS (1,3-1,4)-BETA-GLUCANASE. GEOMETRY, ... -

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Basic information

Entry
Database: PDB / ID: 1glh
TitleCATION BINDING TO A BACILLUS (1,3-1,4)-BETA-GLUCANASE. GEOMETRY, AFFINITY AND EFFECT ON PROTEIN STABILITY
Components1,3-1,4-BETA-GLUCANASE
KeywordsHYDROLASE
Function / homology
Function and homology information


licheninase / licheninase activity / 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 speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKeitel, T. / Heinemann, U.
Citation
Journal: Eur.J.Biochem. / Year: 1994
Title: Cation binding to a Bacillus (1,3-1,4)-beta-glucanase. Geometry, affinity and effect on protein stability
Authors: Keitel, T. / Meldgaard, M. / 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
DepositionNov 25, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,9582
Polymers23,9351
Non-polymers231
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.220, 72.560, 49.970
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-GLUCANASE


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsATOMS IN SODIUM COORDINATION SPHERE: O PRO 9 O GLY 45 O ASP 207 OD1 ASP 207 OH TYR 56 FROM A ...ATOMS IN SODIUM COORDINATION SPHERE: O PRO 9 O GLY 45 O ASP 207 OD1 ASP 207 OH TYR 56 FROM A SYMMETRY-RELATED MOLECULE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Keitel, T., (1991) J. Mol. Biol, 218, 703.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
170 mg/mlprotein1drop
220 mM2-(N-morpholino)ethanesulfonic acid1drop
30.02 %(w/v)1dropNaN3
420 mM2-(N-morpholino)ethanesulfonic acid1reservoir
50.02 %(w/v)1reservoirNaN3
613 %(w/v)PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 13475 / % possible obs: 80.9 % / Observed criterion σ(I): 1

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 1 /
RfactorNum. reflection
Rfree0.225 -
obs0.198 13252
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 1 115 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.552
X-RAY DIFFRACTIONp_mcangle_it2.463
X-RAY DIFFRACTIONp_scbond_it2.393
X-RAY DIFFRACTIONp_scangle_it3.393
X-RAY DIFFRACTIONp_plane_restr0.0090.015
X-RAY DIFFRACTIONp_chiral_restr0.1180.1
X-RAY DIFFRACTIONp_singtor_nbd0.1350.15
X-RAY DIFFRACTIONp_multtor_nbd0.1380.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1280.15
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.83
X-RAY DIFFRACTIONp_staggered_tor17.615
X-RAY DIFFRACTIONp_orthonormal_tor24.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198 / Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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