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- PDB-7eip: Crystal structure of ligand-free chondroitin ABC lyase I -

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Basic information

Entry
Database: PDB / ID: 7eip
TitleCrystal structure of ligand-free chondroitin ABC lyase I
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
ACETATE ION / Chondroitin sulfate ABC endolyase
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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

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Assembly

Deposited unit
A: Chondroitin sulfate ABC endolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3594
Polymers115,2161
Non-polymers1423
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint1 kcal/mol
Surface area36160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.944, 94.239, 229.082
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 787 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.35 %
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: 1.88→50 Å / Num. obs: 87389 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.8
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2 / Num. unique obs: 4384 / CC1/2: 0.73 / % 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: 1.88→43.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.612 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 4349 5 %RANDOM
Rwork0.169 ---
obs0.1711 82946 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.79 Å2 / Biso mean: 27.116 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--1.24 Å20 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 1.88→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 0 9 787 8516
Biso mean--43.55 31.41 -
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0137932
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177141
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.6410762
X-RAY DIFFRACTIONr_angle_other_deg1.451.57516655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6175967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87323.698411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.064151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4521533
X-RAY DIFFRACTIONr_chiral_restr0.090.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021636
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 307 -
Rwork0.256 6027 -
all-6334 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -8.695 Å / Origin y: 25.341 Å / Origin z: -31.847 Å
111213212223313233
T0.0466 Å20.0017 Å2-0.0168 Å2-0.0063 Å2-0.0034 Å2--0.0313 Å2
L0.0639 °2-0.0532 °2-0.0599 °2-0.0628 °20.0896 °2--0.443 °2
S-0.0087 Å °0.0185 Å °-0.0095 Å °0.0042 Å °-0.0165 Å °-0.0106 Å °-0.114 Å °-0.0315 Å °0.0252 Å °

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