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- PDB-7yke: Crystal structure of chondroitin ABC lyase I in complex with chon... -

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Basic information

Entry
Database: PDB / ID: 7yke
TitleCrystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4,6-sulfate
ComponentsChondroitin sulfate ABC endolyase
KeywordsLYASE / Complex / Polysaccharide lyase family 8 / Carbohydrate-binding
Function / homology
Function and homology information


chondroitin-sulfate-ABC endolyase / chondroitin-sulfate-ABC endolyase activity / glycosaminoglycan catabolic process / carbohydrate binding / carbohydrate metabolic process / periplasmic space / extracellular region / metal ion binding
Similarity search - Function
Lyase, N-terminal / Lyase, catalytic / Chondroitin sulfate ABC endolyase / Chondroitin sulfate ABC lyase / Lyase, N terminal / Lyase, catalytic / 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 ...Lyase, N-terminal / Lyase, catalytic / Chondroitin sulfate ABC endolyase / Chondroitin sulfate ABC lyase / Lyase, N terminal / Lyase, catalytic / 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 / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Chondroitin sulfate ABC endolyase
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsTakashima, M. / Watanabe, I. / Miyanaga, A. / Eguchi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2023
Title: Biochemical and crystallographic assessments of the effect of 4,6-O-disulfated disaccharide moieties in chondroitin sulfate E on chondroitinase ABC I activity.
Authors: Watanabe, I. / Miyanaga, A. / Hoshi, H. / Suzuki, K. / Eguchi, T.
History
DepositionJul 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chondroitin sulfate ABC endolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3204
Polymers115,2161
Non-polymers1,1033
Water13,349741
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint5 kcal/mol
Surface area36300 Å2
Unit cell
Length a, b, c (Å)49.069, 94.497, 229.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chondroitin sulfate ABC endolyase / Chondroitin ABC endoeliminase / Chondroitin ABC lyase I / Chondroitin sulfate ABC lyase I / ChS ABC ...Chondroitin ABC endoeliminase / Chondroitin ABC lyase I / Chondroitin sulfate ABC lyase I / ChS ABC lyase I / Chondroitinase ABC I / cABC I / Endochondroitinase ABC


Mass: 115216.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Proteus vulgaris (bacteria)
References: UniProt: P59807, chondroitin-sulfate-ABC endolyase
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4,6-di-O-sulfo-beta-D- ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4,6-di-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 539.443 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc4SO36SO3]{[(3+1)][b-D-4-deoxy-GlcpA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: magnesium acetate, ammonium acetate, polyethylene glycol 3350, HEPES-Na

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2020
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 87996 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.4
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.886 / Num. unique obs: 4419 / CC1/2: 0.736 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EIS

7eis


Resolution: 1.88→49.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.421 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 4380 5 %RANDOM
Rwork0.1692 ---
obs0.1714 83515 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.23 Å2 / Biso mean: 27.84 Å2 / Biso min: 12.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--1.14 Å20 Å2
3----1.49 Å2
Refinement stepCycle: final / Resolution: 1.88→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 0 69 741 8530
Biso mean--40.29 32.71 -
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0137979
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177156
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.65110828
X-RAY DIFFRACTIONr_angle_other_deg1.4741.58316689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5815961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61223.667409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.727151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8731533
X-RAY DIFFRACTIONr_chiral_restr0.1330.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021639
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 323 -
Rwork0.247 6092 -
all-6415 -
obs--99.98 %
Refinement TLS params.Method: refined / Origin x: -8.728 Å / Origin y: -25.274 Å / Origin z: 31.92 Å
111213212223313233
T0.0364 Å20.0021 Å20.0099 Å2-0.009 Å2-0.0037 Å2--0.0246 Å2
L0.0347 °20.039 °20.0358 °2-0.0563 °20.0438 °2--0.2582 °2
S-0.007 Å °-0.0098 Å °0.009 Å °-0.0126 Å °-0.0091 Å °-0.0061 Å °0.0746 Å °-0.0155 Å °0.0161 Å °

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