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- PDB-7czh: PL24 ulvan lyase-Uly1 -

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Basic information

Entry
Database: PDB / ID: 7czh
TitlePL24 ulvan lyase-Uly1
ComponentsUly1
KeywordsLYASE / polysaccharide lyase / ulvan lyase / PL24 / beta-propeller
Function / homologyF5/8 type C domain-containing protein
Function and homology information
Biological speciesCatenovulum maritimum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.104 Å
AuthorsZhang, Y.Z. / Chen, X.L. / Dong, F. / Xu, F.
CitationJournal: Appl.Environ.Microbiol. / Year: 2021
Title: Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24.
Authors: Xu, F. / Dong, F. / Sun, X.H. / Cao, H.Y. / Fu, H.H. / Li, C.Y. / Zhang, X.Y. / McMinn, A. / Zhang, Y.Z. / Wang, P. / Chen, X.L.
History
DepositionSep 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uly1
B: Uly1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,69616
Polymers111,8232
Non-polymers87314
Water16,898938
1
A: Uly1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4008
Polymers55,9121
Non-polymers4897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-13 kcal/mol
Surface area19840 Å2
MethodPISA
2
B: Uly1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2968
Polymers55,9121
Non-polymers3857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-13 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.100, 99.444, 94.996
Angle α, β, γ (deg.)90.000, 90.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uly1 / PL24 ulvan lyase


Mass: 55911.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenovulum maritimum (bacteria) / Gene: XM47_11230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J8GWN9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 938 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM calcium acetate hydrate (pH 6.5), 18% (w/v) polyethylene glycol (PEG) 8000, and 100 mM sodium cacodylate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.104→50 Å / Num. obs: 62242 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.219 / Rrim(I) all: 0.237 / Net I/σ(I): 28.2
Reflection shellResolution: 2.104→2.14 Å / Rmerge(I) obs: 0.337 / Num. unique obs: 3092 / Rrim(I) all: 0.365

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.104→47.496 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 2986 4.8 %
Rwork0.156 59191 -
obs0.1578 62177 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.93 Å2 / Biso mean: 27.0946 Å2 / Biso min: 10.16 Å2
Refinement stepCycle: final / Resolution: 2.104→47.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7714 0 44 938 8696
Biso mean--39.28 33.99 -
Num. residues----962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077965
X-RAY DIFFRACTIONf_angle_d0.80510771
X-RAY DIFFRACTIONf_chiral_restr0.0541118
X-RAY DIFFRACTIONf_plane_restr0.0051388
X-RAY DIFFRACTIONf_dihedral_angle_d13.5364604
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.104-2.1380.23941260.1737234383
2.138-2.17490.26541340.17932853100
2.1749-2.21440.23351600.17922826100
2.2144-2.2570.24921450.1852847100
2.257-2.30310.22261420.18262808100
2.3031-2.35320.21841700.18112787100
2.3532-2.40790.24431660.17992811100
2.4079-2.46810.21771070.17942842100
2.4681-2.53490.23821430.17762864100
2.5349-2.60940.2421610.17912794100
2.6094-2.69370.21351470.17842828100
2.6937-2.78990.21511080.18252886100
2.7899-2.90160.20991160.16672851100
2.9016-3.03370.1911140.16672870100
3.0337-3.19360.19691710.16152828100
3.1936-3.39360.17771330.15312862100
3.3936-3.65550.1961650.14112822100
3.6555-4.02320.1681400.12772839100
4.0232-4.6050.13721560.11372849100
4.605-5.80020.14841370.12822893100
5.8002-47.4960.17841450.1681288899

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