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- PDB-9f9v: Crystal structure of 892_05174 from Planctomycetota strain 892 -

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Basic information

Entry
Database: PDB / ID: 9f9v
TitleCrystal structure of 892_05174 from Planctomycetota strain 892
ComponentsPutative secreted protein
KeywordsHYDROLASE / Fucoidan / endo-fucoidanase / endo-fuconase / GH168 / glycosyl hydrolase
Function / homologyHypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Glycoside hydrolase superfamily / Putative secreted protein
Function and homology information
Biological speciesRhodopirellula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsPerez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Lorizate, M. / Arrizabalaga, U. / Garcia-Alija, M. / Terrones, O. / Contreras, F.X. / Guerin, M.E. / Trastoy, B. / Alonso-Saez, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other government Spain
CitationJournal: Nat Commun / Year: 2024
Title: Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota.
Authors: Perez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Terrones, O. / Arrizabalaga, U. / Garcia-Alija, M. / Lorizate, M. / Martinez Gascuena, A. / Garcia-Alvarez, I. / Nieto-Garai, J.A. / ...Authors: Perez-Cruz, C. / Moraleda-Montoya, A. / Liebana, R. / Terrones, O. / Arrizabalaga, U. / Garcia-Alija, M. / Lorizate, M. / Martinez Gascuena, A. / Garcia-Alvarez, I. / Nieto-Garai, J.A. / Olazar-Intxausti, J. / Rodriguez-Colinas, B. / Mann, E. / Chiara, J.L. / Contreras, F.X. / Guerin, M.E. / Trastoy, B. / Alonso-Saez, L.
History
DepositionMay 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 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: Putative secreted protein
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9067
Polymers85,2562
Non-polymers6515
Water6,521362
1
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8372
Polymers42,6281
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0695
Polymers42,6281
Non-polymers4414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.390, 62.110, 66.900
Angle α, β, γ (deg.)68.830, 88.340, 78.920
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Putative secreted protein


Mass: 42627.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopirellula (bacteria) / Gene: RRSWK_04259 / Production host: Escherichia coli (E. coli) / References: UniProt: M5T2H2
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.98 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 37,5% w/v M1K2230 0.1 M MB2 7.5 pH - Sodium HEPES; MOPS (acid) 0.1 M MCA (complex ingredient) - 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.57→43.52 Å / Num. obs: 87524 / % possible obs: 95.43 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.46 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.86
Reflection shellResolution: 1.57→36.45 Å / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 87100 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→43.52 Å / SU ML: 0.2414 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 4377 5 %
Rwork0.2089 83147 -
obs0.2101 87524 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.78 Å2
Refinement stepCycle: LAST / Resolution: 1.57→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 37 362 6183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275998
X-RAY DIFFRACTIONf_angle_d0.64398157
X-RAY DIFFRACTIONf_chiral_restr0.042838
X-RAY DIFFRACTIONf_plane_restr0.00611051
X-RAY DIFFRACTIONf_dihedral_angle_d8.4464807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.580.40931290.37062448X-RAY DIFFRACTION83.75
1.58-1.60.33431440.32832723X-RAY DIFFRACTION94.25
1.6-1.620.34291440.30672750X-RAY DIFFRACTION95.04
1.62-1.640.31361470.29522794X-RAY DIFFRACTION94.6
1.64-1.660.36991450.29432750X-RAY DIFFRACTION94.92
1.66-1.690.35321460.2882780X-RAY DIFFRACTION95.09
1.69-1.710.30781470.28652788X-RAY DIFFRACTION95.35
1.71-1.740.32431450.27832756X-RAY DIFFRACTION94.77
1.74-1.760.3041470.28072794X-RAY DIFFRACTION95.43
1.76-1.790.28731450.26072738X-RAY DIFFRACTION94.84
1.79-1.820.29161460.25452790X-RAY DIFFRACTION95.32
1.82-1.860.31811470.24532793X-RAY DIFFRACTION95.39
1.86-1.890.27141450.25292742X-RAY DIFFRACTION95.31
1.89-1.930.30171500.24592858X-RAY DIFFRACTION95.58
1.93-1.970.25841450.23432756X-RAY DIFFRACTION95.36
1.97-2.020.26991460.23362775X-RAY DIFFRACTION95.68
2.02-2.070.27631450.22222749X-RAY DIFFRACTION95.42
2.07-2.120.26521470.2262799X-RAY DIFFRACTION95.43
2.12-2.190.23451470.21662791X-RAY DIFFRACTION95.58
2.19-2.260.24771450.22222773X-RAY DIFFRACTION95.27
2.26-2.340.23951480.21572800X-RAY DIFFRACTION95.65
2.34-2.430.25691450.20742766X-RAY DIFFRACTION95.63
2.43-2.540.23681480.22182808X-RAY DIFFRACTION96.41
2.54-2.680.25591490.20842823X-RAY DIFFRACTION95.81
2.68-2.840.22961460.21632785X-RAY DIFFRACTION96.8
2.84-3.060.22061470.20612793X-RAY DIFFRACTION96.24
3.06-3.370.21141490.18872820X-RAY DIFFRACTION96.62
3.37-3.860.18241470.1712785X-RAY DIFFRACTION95.38
3.86-4.860.18271480.15992809X-RAY DIFFRACTION95.82
4.86-43.520.18891480.18742811X-RAY DIFFRACTION96.51

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