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- PDB-6hr5: Structure of the S1_25 family sulfatase module of the rhamnosidas... -

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Basic information

Entry
Database: PDB / ID: 6hr5
TitleStructure of the S1_25 family sulfatase module of the rhamnosidase FA22250 from Formosa agariphila
ComponentsAlpha-L-rhamnosidase/sulfatase (GH78)
KeywordsHYDROLASE / algal polysaccharide carrageenan sulfatase
Function / homology
Function and homology information


alpha-L-rhamnosidase / alpha-L-rhamnosidase activity / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / carbohydrate metabolic process / periplasmic space / metal ion binding
Similarity search - Function
Alpha-L-rhamnosidase C-terminal domain / Bacterial alpha-L-rhamnosidase C-terminal domain / Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatase, N-terminal / Sulfatase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Alkaline-phosphatase-like, core domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Bifunctional sulfatase/alpha-L-rhamnosidase
Similarity search - Component
Biological speciesFormosa agariphila KMM 3901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.912 Å
AuthorsRoret, T. / Prechoux, A. / Czjzek, M. / Michel, G.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE19- 0020-01 France
French National Research AgencyANR-10-BTBR-04 France
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan.
Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, ...Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, M.D. / Trautwein-Schult, A. / Becher, D. / Schweder, T. / Bornscheuer, U.T. / Hehemann, J.H.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-L-rhamnosidase/sulfatase (GH78)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3792
Polymers54,3391
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.879, 48.871, 92.651
Angle α, β, γ (deg.)90.00, 105.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-L-rhamnosidase/sulfatase (GH78)


Mass: 54338.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Formosa agariphila KMM 3901 (bacteria) / Gene: BN863_22250 / Production host: Escherichia coli (E. coli) / References: UniProt: T2KM26
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 2000MME 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.91→48.87 Å / Num. obs: 10211 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.982 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.105 / Rrim(I) all: 0.277 / Net I/σ(I): 7
Reflection shellResolution: 2.91→3.09 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.163 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1605 / CC1/2: 0.801 / Rpim(I) all: 0.471 / Rrim(I) all: 1.257 / % possible all: 97.9

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Processing

Software
NameVersionClassification
XDSJanuary 26, 2018data reduction
Aimless7.0.063data scaling
Coot0.8.9model building
MOLREP7.0.063phasing
PHENIX1.13-2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.912→44.609 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.21
RfactorNum. reflection% reflection
Rfree0.3608 533 5.23 %
Rwork0.3216 --
obs0.3237 10183 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.912→44.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 1 0 3077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053143
X-RAY DIFFRACTIONf_angle_d1.0054243
X-RAY DIFFRACTIONf_dihedral_angle_d6.2751885
X-RAY DIFFRACTIONf_chiral_restr0.054452
X-RAY DIFFRACTIONf_plane_restr0.006547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9117-3.20460.42921380.38272353X-RAY DIFFRACTION99
3.2046-3.66820.33711190.32832398X-RAY DIFFRACTION100
3.6682-4.62070.34251250.3032430X-RAY DIFFRACTION100
4.6207-44.61440.36221510.31032469X-RAY DIFFRACTION100

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