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- PDB-1gbg: BACILLUS LICHENIFORMIS BETA-GLUCANASE -

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Basic information

Entry
Database: PDB / ID: 1gbg
TitleBACILLUS LICHENIFORMIS BETA-GLUCANASE
Components(1,3-1,4)-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 speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHahn, M. / Heinemann, U.
Citation
Journal: FEBS Lett. / Year: 1995
Title: Crystal structure of Bacillus licheniformis 1,3-1,4-beta-D-glucan 4-glucanohydrolase at 1.8 A resolution.
Authors: Hahn, M. / Pons, J. / Planas, A. / Querol, E. / 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.
#2: Journal: Eur.J.Biochem. / Year: 1991
Title: Molecular Cloning, Expression and Nucleotide Sequence of the Endo-Beta-1,3-1,4-D-Glucanase Gene from Bacillus Licheniformis
Authors: Lloberas, J. / Perez-Pons, J.A. / Querol, E.
History
DepositionAug 25, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / struct_conn / struct_ref_seq_dif / 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 / _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_ref_seq_dif.details / _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)24,4152
Polymers24,3751
Non-polymers401
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.330, 39.130, 43.880
Angle α, β, γ (deg.)64.66, 105.86, 110.68
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO 201

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Components

#1: Protein (1,3-1,4)-BETA-D-GLUCAN 4 GLUCANOHYDROLASE / BETA-GLUCANASE / LICHENASE


Mass: 24374.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Plasmid: PBR328 / Production host: Escherichia coli (E. coli) / References: UniProt: P27051, 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.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBOND LENGTHS OF SIDE CHAINS OF GLU AND ASP FOLLOW THE TNT STANDARD FOR PROTONATED CARBOXY GROUPS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
144 mg/mlprotein 1drop
22 mM1dropCaCl2
320 %PEG80001reservoir
42 mM1reservoirCaCl2
550 mMpotassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 17238 / % possible obs: 94.6 % / Rmerge(I) obs: 0.082

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Processing

Software
NameClassification
MOSFLM/MADNESdata collection
TNTrefinement
MOSFLMdata reduction
MADNESdata reduction
RefinementResolution: 1.8→6 Å / σ(F): 2
Details: ASN 28 IS IN CONTACT WITH A NEIGHBORING MOLECULE. THEREFORE ITS DIHEDRAL ANGLES LIE OUTSIDE THE EXPECTED RANGE.
RfactorNum. reflection
Rfree0.236 -
obs0.165 16792
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 1 158 1883
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.004
X-RAY DIFFRACTIONt_angle_deg1.8
X-RAY DIFFRACTIONt_dihedral_angle_d26.09
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.005
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd16
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.165 / Rfactor Rfree: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg26.09

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