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

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Basic information

Entry
Database: PDB / ID: 7eiq
TitleCrystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4S
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: 1.8 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)116,6195
Polymers115,2161
Non-polymers1,4024
Water14,826823
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint26 kcal/mol
Surface area36340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.272, 94.528, 229.231
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-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 459.380 Da / Num. of mol.: 3
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][a21eEA-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-2-deoxy-Galp4SO3]{[(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.: 823 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 7, 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: 1.8→50 Å / Num. obs: 100438 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2 / Num. unique obs: 4953 / CC1/2: 0.711 / % 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: 1.8→49.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.812 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 5115 5.1 %RANDOM
Rwork0.1712 ---
obs0.1734 95220 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.59 Å2 / Biso mean: 27.233 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--1.05 Å20 Å2
3----1.92 Å2
Refinement stepCycle: final / Resolution: 1.8→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 0 91 823 8634
Biso mean--33.94 31.45 -
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0138022
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177186
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.65710893
X-RAY DIFFRACTIONr_angle_other_deg1.5111.58516772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7335967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49123.683410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.264151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6171533
X-RAY DIFFRACTIONr_chiral_restr0.1140.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021649
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 365 -
Rwork0.266 7004 -
all-7369 -
obs--99.99 %
Refinement TLS params.Method: refined / Origin x: -8.587 Å / Origin y: 25.144 Å / Origin z: -31.967 Å
111213212223313233
T0.0584 Å20.0031 Å2-0.0254 Å2-0.005 Å20.0005 Å2--0.1058 Å2
L0.1638 °2-0.0739 °2-0.1149 °2-0.1408 °20.0939 °2--0.6708 °2
S-0.0045 Å °0.0224 Å °-0.0003 Å °0.017 Å °-0.0156 Å °-0.0301 Å °-0.1644 Å °-0.0377 Å °0.0201 Å °

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