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- PDB-1dbo: CRYSTAL STRUCTURE OF CHONDROITINASE B -

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Basic information

Entry
Database: PDB / ID: 1dbo
TitleCRYSTAL STRUCTURE OF CHONDROITINASE B
ComponentsCHONDROITINASE B
KeywordsLYASE / ACTIVE SITE / BETA-ELIMINATION / DEMATAN SULFATE
Function / homology
Function and homology information


chondroitin B lyase / chondroitin B lyase activity
Similarity search - Function
PL-6 family / Chondroitinase B / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
: / Chondroitinase-B
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsHuang, W. / Matte, A. / Li, Y. / Kim, Y.S. / Linhardt, R.J. / Su, H. / Cygler, M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution.
Authors: Huang, W. / Matte, A. / Li, Y. / Kim, Y.S. / Linhardt, R.J. / Su, H. / Cygler, M.
History
DepositionNov 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 16, 2015Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _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.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHONDROITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9573
Polymers56,3921
Non-polymers1,5642
Water8,557475
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.600, 74.400, 58.700
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHONDROITINASE B


Mass: 56392.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pedobacter heparinus (bacteria) / References: GenBank: U27584, UniProt: Q46079*PLUS
#2: Polysaccharide 4-deoxy-alpha-D-glucopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-beta-L-fucopyranose-(1-4) ...4-deoxy-alpha-D-glucopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 1102.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/7,7,6/[a1122h-1a_1-5][a2122A-1a_1-5][a212h-1b_1-5][a1221m-1b_1-5_2*OC][a21d2h-1a_1-5][a2122h-1b_1-5][a2211m-1a_1-5]/1-2-3-4-5-6-7/a2-b1_a4-g1_b4-c1_c4-d1_d3-e1_d4-f1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-Manp]{[(2+1)][a-D-GlcpA]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Arap2Me]{[(3+1)][a-D-4-deoxy-Glcp]{}[(4+1)][b-D-Glcp]{}}}}[(4+1)][a-L-Rhap]{}}}LINUCSPDB-CARE
#3: Polysaccharide 4-deoxy-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 461.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O][a21d2A-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc4SO3]{[(3+1)][b-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 34.8652 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.7
Details: PEG8000, 2-METHYL-2,4-PENTADIOL, AMMONIUM ACETATE, TRIS, pH 8.7, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: Li, Y., (1999) Acta Crystallog. Sect., D55, 1055.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-8 mg/mlprotein1drop
219 %(w/v)PEG80001reservoir
3100 mMBicine1reservoir
4100 mMTris-HCl1reservoir
50.15 Mammonium acetate1reservoir
615 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 44142 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.129 / % possible all: 57.8
Reflection
*PLUS
Num. obs: 44142 / Num. measured all: 135533
Reflection shell
*PLUS
% possible obs: 57.8 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→19.95 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.217 1333 RANDOM
Rwork0.181 --
obs0.178 44083 -
all-47848 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.249 Å20 Å20.393 Å2
2--0.515 Å20 Å2
3----0.265 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 103 475 4361
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.75
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE_REP.PARAM
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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