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

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Basic information

Entry
Database: PDB / ID: 7eir
TitleCrystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 6S
ComponentsChondroitin sulfate ABC endolyase
KeywordsLYASE / 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: 1.92 Å
AuthorsTakashima, M. / Miyanaga, A. / Eguchi, T.
CitationJournal: Glycobiology / Year: 2021
Title: Substrate specificity of Chondroitinase ABC I based on analyses of biochemical reactions and crystal structures in complex with disaccharides.
Authors: Takashima, M. / Watanabe, I. / Miyanaga, A. / Eguchi, T.
History
DepositionMar 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Chondroitin sulfate ABC endolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2525
Polymers115,2161
Non-polymers1,0354
Water14,862825
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint18 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.324, 94.776, 229.497
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-6-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 459.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O_6*OSO/3=O/3=O][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-2-deoxy-Galp6SO3]{[(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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
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 S 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: 1.92→50 Å / Num. obs: 83417 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.128 / Net I/σ(I): 10.3
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4522 / CC1/2: 0.746 / % 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: 1HN0

1hn0


Resolution: 1.92→49.13 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 4243 5.1 %RANDOM
Rwork0.1659 ---
obs0.1681 79080 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.96 Å2 / Biso mean: 33.049 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--1.15 Å20 Å2
3----1.7 Å2
Refinement stepCycle: final / Resolution: 1.92→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 0 67 825 8612
Biso mean--50.24 32.05 -
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137998
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177175
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.65110853
X-RAY DIFFRACTIONr_angle_other_deg2.381.58116740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5335965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07523.683410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.614151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9421533
X-RAY DIFFRACTIONr_chiral_restr0.1150.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028886
X-RAY DIFFRACTIONr_gen_planes_other0.0160.021645
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 326 -
Rwork0.242 5784 -
all-6110 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.932 Å / Origin y: -25.432 Å / Origin z: 31.893 Å
111213212223313233
T0.0704 Å20.0029 Å20.0205 Å2-0.0019 Å2-0.0009 Å2--0.0445 Å2
L0.069 °20.0618 °20.0904 °2-0.0883 °20.0594 °2--0.3775 °2
S-0.002 Å °-0.0098 Å °0.0136 Å °-0.0236 Å °-0.0117 Å °-0.0204 Å °0.114 Å °-0.0054 Å °0.0137 Å °

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