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- PDB-8khw: The crystal structure of glycosaminoglycan lyase GAGase VII -

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Basic information

Entry
Database: PDB / ID: 8khw
TitleThe crystal structure of glycosaminoglycan lyase GAGase VII
ComponentsDUF4962 domain-containing protein
KeywordsLYASE / Glycosaminoglycan / PL_35
Function / homologyHeparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / lyase activity / : / DUF4962 domain-containing protein
Function and homology information
Biological speciesBacteroides intestinalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWei, L. / Cao, H.Y. / Li, F.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31570071 China
National Science Foundation (NSF, China)31971201 China
CitationJournal: To Be Published
Title: The crystal structure of glycosaminoglycan lyase GAGase VII
Authors: Wei, L. / Cao, H.Y. / Li, F.C.
History
DepositionAug 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4962 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1912
Polymers70,1361
Non-polymers551
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.407, 98.407, 134.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DUF4962 domain-containing protein


Mass: 70135.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis (bacteria) / Gene: EAJ06_20265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V1YUP8
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES (pH 7.0), 36% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→19.87 Å / Num. obs: 49305 / % possible obs: 99.68 % / Redundancy: 23.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.02 / Rrim(I) all: 0.1 / Net I/σ(I): 20.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2737 / CC1/2: 0.966 / Rpim(I) all: 0.158 / Rrim(I) all: 0.737 / % possible all: 99.85

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.87 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 3714 7.53 %
Rwork0.2074 --
obs0.2122 49305 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 1 41 4674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084737
X-RAY DIFFRACTIONf_angle_d0.9866431
X-RAY DIFFRACTIONf_dihedral_angle_d6.673635
X-RAY DIFFRACTIONf_chiral_restr0.053702
X-RAY DIFFRACTIONf_plane_restr0.006824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.40391380.27611665X-RAY DIFFRACTION100
2.43-2.460.36661420.25341706X-RAY DIFFRACTION100
2.46-2.50.32331380.25751685X-RAY DIFFRACTION100
2.5-2.530.35821410.26021704X-RAY DIFFRACTION100
2.53-2.570.40541340.25141667X-RAY DIFFRACTION100
2.57-2.610.34041340.26531677X-RAY DIFFRACTION100
2.61-2.650.41891390.23191739X-RAY DIFFRACTION100
2.65-2.70.31851330.24861628X-RAY DIFFRACTION100
2.7-2.750.35381390.23691707X-RAY DIFFRACTION100
2.75-2.80.31551370.24671690X-RAY DIFFRACTION100
2.8-2.860.32581360.23431681X-RAY DIFFRACTION100
2.86-2.920.2831460.23611690X-RAY DIFFRACTION100
2.92-2.990.3151340.23731692X-RAY DIFFRACTION100
2.99-3.060.31581330.23941699X-RAY DIFFRACTION100
3.06-3.140.30651390.24671696X-RAY DIFFRACTION100
3.14-3.230.28151350.24421672X-RAY DIFFRACTION100
3.24-3.340.37221420.24121699X-RAY DIFFRACTION100
3.34-3.460.29061380.22411695X-RAY DIFFRACTION100
3.46-3.60.30681360.2131685X-RAY DIFFRACTION100
3.6-3.760.23961300.20781667X-RAY DIFFRACTION100
3.76-3.950.28641400.20811714X-RAY DIFFRACTION100
3.95-4.20.24811350.1791681X-RAY DIFFRACTION100
4.2-4.520.19671360.17751710X-RAY DIFFRACTION100
4.52-4.970.19611420.15461691X-RAY DIFFRACTION100
4.97-5.670.21241410.18481661X-RAY DIFFRACTION100
5.67-7.090.2671390.19161704X-RAY DIFFRACTION100
7.1-19.870.21351370.16831686X-RAY DIFFRACTION100

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