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- PDB-8khv: The crystal structure of glycosaminoglycan lyase GAGase II -

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Basic information

Entry
Database: PDB / ID: 8khv
TitleThe crystal structure of glycosaminoglycan lyase GAGase II
ComponentsHeparinase II/III-like protein
KeywordsLYASE / Glycosaminoglycan / PL_35
Function / homologyHeparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / lyase activity / : / Heparinase II/III-like protein
Function and homology information
Biological speciesSpirosoma fluviale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: Heparinase II/III-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6315
Polymers68,4551
Non-polymers1754
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.917, 82.096, 79.885
Angle α, β, γ (deg.)90.000, 106.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heparinase II/III-like protein


Mass: 68455.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirosoma fluviale (bacteria) / Gene: SAMN06269250_2316 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A286FIB6
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.0), 12% (w/v) polyethylene glycol (PEG) 6000 and 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→44.01 Å / Num. obs: 86421 / % possible obs: 98.55 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 4092 / CC1/2: 0.964 / Rpim(I) all: 0.1 / Rrim(I) all: 0.23 / % possible all: 92.04

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→44.01 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1924 3905 4.52 %
Rwork0.1587 82516 -
obs0.1602 86421 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.81 Å2 / Biso mean: 13.383 Å2 / Biso min: 1.67 Å2
Refinement stepCycle: final / Resolution: 1.9→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 4 644 5177
Biso mean--21.7 25.47 -
Num. residues----579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.26021180.17732618273687
1.92-1.950.21341230.16932748287190
1.95-1.970.21971320.16512838297095
1.97-20.19561410.16462981312297
2-2.030.26691380.16212882302099
2.03-2.060.23011390.15683034317399
2.06-2.090.19951410.1632997313899
2.09-2.130.18911380.15412953309199
2.13-2.160.1991450.15743021316699
2.16-2.20.17961430.14852949309299
2.2-2.240.21051380.15572937307599
2.24-2.290.22041450.16393016316198
2.29-2.340.21981350.16042928306398
2.34-2.390.20121420.15362979312199
2.39-2.450.21381400.15542928306899
2.45-2.520.16621480.15393019316799
2.52-2.590.15581400.15012956309699
2.59-2.680.19211430.15442989313299
2.68-2.770.19151370.15952957309498
2.77-2.880.22391370.16032942307998
2.88-3.020.23641400.15793020316099
3.02-3.170.19711380.16112953309199
3.18-3.370.17311410.158530003141100
3.37-3.630.18941440.15332994313899
3.63-40.14921440.15112960310499
4-4.580.15371480.14243005315399
4.58-5.760.18171380.16162971310999
5.77-44.010.1921490.19662941309099

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