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- PDB-6ptm: Crystal structure of apo exo-carrageenase GH42 from Bacteroides ovatus -

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Basic information

Entry
Database: PDB / ID: 6ptm
TitleCrystal structure of apo exo-carrageenase GH42 from Bacteroides ovatus
ComponentsUncharacterized protein
KeywordsHYDROLASE / exo-carrageenase
Function / homologyGlycoside hydrolase, family 42, N-terminal / Beta-galactosidase / beta-galactosidase complex / beta-galactosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Glyco_hydro_42 domain-containing protein
Function and homology information
Biological speciesBacteroides ovatus CL02T12C04 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsHettle, A.G. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Commun Biol / Year: 2019
Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.
Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 13, 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

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9036
Polymers88,5931
Non-polymers3105
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.240, 109.690, 126.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 88592.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus CL02T12C04 (bacteria)
Gene: HMPREF1069_02044 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I8YN04
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 400, Tris, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.1271 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2→54.66 Å / Num. obs: 57229 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4129

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→50.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.534 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 2874 5 %RANDOM
Rwork0.1654 ---
obs0.1672 54286 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.36 Å2 / Biso mean: 20.083 Å2 / Biso min: 10.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 2→50.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5789 0 20 418 6227
Biso mean--26.71 24.38 -
Num. residues----726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175446
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.6428079
X-RAY DIFFRACTIONr_angle_other_deg1.4281.57712675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8825732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56323.562306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.121151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7881527
X-RAY DIFFRACTIONr_chiral_restr0.080.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021233
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 185 -
Rwork0.233 3939 -
all-4124 -
obs--99.28 %

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