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- PDB-5opq: A 3,6-anhydro-D-galactosidase produced by Zobellia galactanivoran... -

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Basic information

Entry
Database: PDB / ID: 5opq
TitleA 3,6-anhydro-D-galactosidase produced by Zobellia galactanivorans. This is an exo-lytic enzyme that hydrolyzes terminal 3,6-anhydro-D-galactose from the non-reducing end of carrageenan oligosaccharides.
Components3,6-anhydro-D-galactosidase
KeywordsHYDROLASE / glycoside hydrolase 3 / 6-anhydro-D-galactosidase 3 / 6-anhydro-D-galactose carrageenan Zobellia galactanivorans
Function / homologyProtein of unknown function DUF5696 / Family of unknown function (DUF5696) / Conserved hypothetical periplasmic protein
Function and homology information
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsFicko-Blean, E. / Michel, G. / Czjzek, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE19-0020-01 France
CitationJournal: Nat Commun / Year: 2017
Title: Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria.
Authors: Ficko-Blean, E. / Prechoux, A. / Thomas, F. / Rochat, T. / Larocque, R. / Zhu, Y. / Stam, M. / Genicot, S. / Jam, M. / Calteau, A. / Viart, B. / Ropartz, D. / Perez-Pascual, D. / Correc, G. ...Authors: Ficko-Blean, E. / Prechoux, A. / Thomas, F. / Rochat, T. / Larocque, R. / Zhu, Y. / Stam, M. / Genicot, S. / Jam, M. / Calteau, A. / Viart, B. / Ropartz, D. / Perez-Pascual, D. / Correc, G. / Matard-Mann, M. / Stubbs, K.A. / Rogniaux, H. / Jeudy, A. / Barbeyron, T. / Medigue, C. / Czjzek, M. / Vallenet, D. / McBride, M.J. / Duchaud, E. / Michel, G.
History
DepositionAug 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 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: 3,6-anhydro-D-galactosidase
B: 3,6-anhydro-D-galactosidase
C: 3,6-anhydro-D-galactosidase
D: 3,6-anhydro-D-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,08518
Polymers311,7424
Non-polymers1,34314
Water50,3342794
1
A: 3,6-anhydro-D-galactosidase
B: 3,6-anhydro-D-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5409
Polymers155,8712
Non-polymers6707
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-95 kcal/mol
Surface area42530 Å2
MethodPISA
2
C: 3,6-anhydro-D-galactosidase
D: 3,6-anhydro-D-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5449
Polymers155,8712
Non-polymers6747
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-78 kcal/mol
Surface area42540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.000, 107.500, 165.800
Angle α, β, γ (deg.)90.00, 114.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-878-

HOH

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Components

#1: Protein
3,6-anhydro-D-galactosidase


Mass: 77935.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: zobellia_3152 / Production host: Escherichia coli (E. coli) / References: UniProt: G0L004
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2794 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 1:1 ratio of 0.14M Na/K-tartrate, 12% PEG 3350 with 9 mg/ml ZGAL_3152

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.7→46.7 Å / Num. obs: 389746 / % possible obs: 99.6 % / Redundancy: 3.1 % / Net I/σ(I): 16.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→46.7 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.567 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17571 19548 5 %RANDOM
Rwork0.14572 ---
obs0.14724 368616 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.04 Å2
2---0.16 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.7→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20834 0 84 2794 23712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01921601
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220144
X-RAY DIFFRACTIONr_angle_refined_deg2.2891.95229264
X-RAY DIFFRACTIONr_angle_other_deg1.008346412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88252663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36124.3921020
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.377153600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77915100
X-RAY DIFFRACTIONr_chiral_restr0.1530.23082
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02124714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9281.88110616
X-RAY DIFFRACTIONr_mcbond_other1.9271.88110606
X-RAY DIFFRACTIONr_mcangle_it2.4312.81913276
X-RAY DIFFRACTIONr_mcangle_other2.4312.81913277
X-RAY DIFFRACTIONr_scbond_it3.2292.11810985
X-RAY DIFFRACTIONr_scbond_other3.2292.11810985
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7033.05815986
X-RAY DIFFRACTIONr_long_range_B_refined6.17516.47627207
X-RAY DIFFRACTIONr_long_range_B_other6.17516.47627208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 1388 -
Rwork0.278 26867 -
obs--98.48 %

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