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- PDB-1qgi: CHITOSANASE FROM BACILLUS CIRCULANS -

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Basic information

Entry
Database: PDB / ID: 1qgi
TitleCHITOSANASE FROM BACILLUS CIRCULANS
ComponentsPROTEIN (CHITOSANASE)
KeywordsHYDROLASE / CHITOSAN DEGRADATION
Function / homology
Function and homology information


chitosanase / chitosanase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitosanase; Chain A, domain 2 / Chitosanase, subunit A, domain 2 / Chitosanases families 46 and 80 active sites signature. / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily / Up-down Bundle ...Chitosanase; Chain A, domain 2 / Chitosanase, subunit A, domain 2 / Chitosanases families 46 and 80 active sites signature. / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSaito, J. / Kita, A. / Higuchi, Y. / Nagata, Y. / Ando, A. / Miki, K.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of chitosanase from Bacillus circulans MH-K1 at 1.6-A resolution and its substrate recognition mechanism.
Authors: Saito, J. / Kita, A. / Higuchi, Y. / Nagata, Y. / Ando, A. / Miki, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Chitosanase from Bacillus Circulans Mh-K1
Authors: Saito, J. / Kita, A. / Nagata, Y. / Ando, A. / Miki, K.
History
DepositionApr 28, 1999Deposition site: PDBE / Processing site: NDB
Revision 1.0Oct 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CHITOSANASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6273
Polymers28,9871
Non-polymers6402
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.300, 128.000, 57.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-500-

SO4

21A-327-

HOH

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Components

#1: Protein PROTEIN (CHITOSANASE)


Mass: 28987.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: MH-K1 / Production host: Brevibacillus brevis (bacteria) / Strain (production host): 47-5Q / References: UniProt: P33673, chitosanase
#2: Polysaccharide 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2- ...2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 543.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*N]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-4-deoxy-GlcpN]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.39 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
165 %(w/v)ammonium sulfate1drop
275 %(w/v)ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.0000,1.0721,1.0722,1.0728
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.07211
31.07221
41.07281
ReflectionResolution: 1.6→50 Å / Num. obs: 40769 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.085
Reflection
*PLUS
Num. measured all: 462029
Reflection shell
*PLUS
% possible obs: 83.7 % / Rmerge(I) obs: 0.656

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.6→5 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE COORDINATES OF SUBSTRATE MOLECULE MADE UP OF TWO MOLECULES OF D-GLUCOSAMINE AND ONE MOLECULE OF N-ACETYL-D-GLUCOSAMINE ARE ESTIMATED COORDINATES BASED ON DOCKING EXPERIMENTS AND WERE NOT ...Details: THE COORDINATES OF SUBSTRATE MOLECULE MADE UP OF TWO MOLECULES OF D-GLUCOSAMINE AND ONE MOLECULE OF N-ACETYL-D-GLUCOSAMINE ARE ESTIMATED COORDINATES BASED ON DOCKING EXPERIMENTS AND WERE NOT PART OF THE CRYSTALLOGRAPHIC DETERMINATION THE SHORT CONTACTS BETWEEN WATER MOLECULES AND THE SUBSTRATE MOLECULE LISTED IN THIS FILE ARE DUE THE FACT THAT THE CRYSTAL STRUCTURE DID NOT CONTAIN SUBSTRATE MOLECULE AND THIS SITE WAS OCCUPIED BY WATER MOLECULES
RfactorNum. reflection% reflection
Rfree0.235 --
Rwork0.192 --
obs-38353 94.2 %
Displacement parametersBiso mean: 20.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 39 150 2226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.375
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.281
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.281

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