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- PDB-1rwg: Crystal structure of Arthrobacter aurescens chondroitin AC lyase ... -

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Basic information

Entry
Database: PDB / ID: 1rwg
TitleCrystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide
Componentschondroitin AC lyase
KeywordsLYASE / chondroitinase / chondroitin / chondroitin lyase
Function / homology
Function and homology information


carbohydrate binding / lyase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 ...Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Chondroitinase (Chondroitin lyase)
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLunin, V.V. / Li, Y. / Miyazono, H. / Kyogashima, M. / Bell, A.W. / Cygler, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism
Authors: Lunin, V.V. / Li, Y. / Linhardt, R.J. / Miyazono, H. / Kyogashima, M. / Kaneko, T. / Bell, A.W. / Cygler, M.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Other
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_angle / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN SUGAR CHAIN D (GAD 809)-(NGL 810)-(GCT 811)-(NGL 812) IS CHONDROITIN SULFATE TETRASACCHARIDE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chondroitin AC lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8524
Polymers79,8641
Non-polymers9893
Water19,1141061
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.683, 86.449, 80.566
Angle α, β, γ (deg.)90.00, 106.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein chondroitin AC lyase /


Mass: 79863.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arthrobacter aurescens (bacteria) / References: UniProt: P84141, chondroitin AC lyase
#2: Polysaccharide 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D- ...2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-2,6-anhydro-3-deoxy-L-xylo-hexonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 870.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O][a2112A-1b_1-5][a21eEA-1a_1-5]/1-2-1-3/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][a-L-4-deoxy-IdopA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 8000, ammonium acetate, glycerol, phosphate buffer, 10 minutes soaking time, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 120769 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rsym value: 0.077 / Net I/σ(I): 9.2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.08refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RW9

1rw9


Resolution: 1.5→28.06 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.993 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17267 1221 1 %RANDOM
Rwork0.13629 ---
obs0.13664 119480 100 %-
all-119480 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.336 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20.33 Å2
2---0.31 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 66 1061 6727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0215817
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9497931
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3323.476233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05915868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8341539
X-RAY DIFFRACTIONr_chiral_restr0.1260.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024405
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22899
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2799
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2160.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7751.53726
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4725938
X-RAY DIFFRACTIONr_scbond_it3.18632091
X-RAY DIFFRACTIONr_scangle_it4.2914.51993
X-RAY DIFFRACTIONr_rigid_bond_restr1.725817
X-RAY DIFFRACTIONr_sphericity_free6.26221061
X-RAY DIFFRACTIONr_sphericity_bonded5.55825693
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 94
Rwork0.188 8723

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