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- PDB-9vtk: Structure of the family PL40 Ulvan Lyase Uly1040 -

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Basic information

Entry
Database: PDB / ID: 9vtk
TitleStructure of the family PL40 Ulvan Lyase Uly1040
ComponentsUly1040
KeywordsLYASE / Polysaccharide lyase / Family PL40 Ulvan lyase
Function / homology: / :
Function and homology information
Biological speciesAlteromonas abrolhosensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWang, H.Q. / Suo, C.L. / Wang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170127 China
National Natural Science Foundation of China (NSFC)32370136 China
CitationJournal: To Be Published
Title: Structure of the family PL40 Ulvan Lyase Uly1040
Authors: Wang, H.Q. / Suo, C.L. / Wang, P.
History
DepositionJul 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uly1040
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,82410
Polymers97,2401
Non-polymers5849
Water10,935607
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)48.997, 126.039, 69.737
Angle α, β, γ (deg.)90.000, 97.960, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uly1040


Mass: 97240.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas abrolhosensis (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 616 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: Sodium bromide, Bis Tris Propone (pH8.7), PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.74→48.56 Å / Num. obs: 84856 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.8
Reflection shellResolution: 1.74→1.79 Å / Rmerge(I) obs: 1.363 / Num. unique obs: 6162

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→37.35 Å / SU ML: 0.2462 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.3159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 4318 5.1 %
Rwork0.1831 80347 -
obs0.1854 84665 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.27 Å2
Refinement stepCycle: LAST / Resolution: 1.74→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6467 0 29 607 7103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01156651
X-RAY DIFFRACTIONf_angle_d1.14019022
X-RAY DIFFRACTIONf_chiral_restr0.0596961
X-RAY DIFFRACTIONf_plane_restr0.01031175
X-RAY DIFFRACTIONf_dihedral_angle_d7.1931885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.38931430.34072448X-RAY DIFFRACTION90.75
1.76-1.780.35411350.32412635X-RAY DIFFRACTION97.3
1.78-1.80.38211510.29092615X-RAY DIFFRACTION97.67
1.8-1.820.37091300.30082676X-RAY DIFFRACTION97.67
1.82-1.850.31781360.2832648X-RAY DIFFRACTION97.89
1.85-1.870.34731510.26662641X-RAY DIFFRACTION98.38
1.87-1.90.28041500.25342681X-RAY DIFFRACTION98.13
1.9-1.930.29011490.23432616X-RAY DIFFRACTION97.74
1.93-1.960.24961320.21452697X-RAY DIFFRACTION98.78
1.96-1.990.26161420.21132658X-RAY DIFFRACTION97.97
1.99-2.020.24541400.21462677X-RAY DIFFRACTION99.37
2.02-2.060.28671250.21072676X-RAY DIFFRACTION97.97
2.06-2.10.26511520.21762688X-RAY DIFFRACTION99.13
2.1-2.140.27361280.20892693X-RAY DIFFRACTION98.88
2.14-2.190.24841320.20842667X-RAY DIFFRACTION98.38
2.19-2.240.27741190.19512749X-RAY DIFFRACTION99.2
2.24-2.30.24231350.19482666X-RAY DIFFRACTION99.43
2.3-2.360.26371250.18452719X-RAY DIFFRACTION98.96
2.36-2.430.22871470.18442692X-RAY DIFFRACTION99.16
2.43-2.510.24111370.17882695X-RAY DIFFRACTION99.33
2.51-2.60.22621490.18532710X-RAY DIFFRACTION99.41
2.6-2.70.23071540.17972689X-RAY DIFFRACTION99.51
2.7-2.820.23871520.18482689X-RAY DIFFRACTION99.58
2.82-2.970.24151660.19082679X-RAY DIFFRACTION99.79
2.97-3.160.2361760.18352684X-RAY DIFFRACTION99.72
3.16-3.40.24421470.16842716X-RAY DIFFRACTION99.72
3.4-3.740.19451610.15212733X-RAY DIFFRACTION99.83
3.75-4.290.18191380.12992715X-RAY DIFFRACTION99.96
4.29-5.40.13141610.12172738X-RAY DIFFRACTION99.93
5.4-37.350.1511550.14692757X-RAY DIFFRACTION99.76

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