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- PDB-5olp: Galacturonidase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5olp
TitleGalacturonidase
ComponentsPectate lyase
KeywordsHYDROLASE / Galacturonidase involved in the degradation of dietary pectic glycans in the human gut.
Function / homology
Function and homology information


polygalacturonase activity / alpha-galactosidase activity / carbohydrate metabolic process / lyase activity
Similarity search - Function
: / Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Pectate lyase superfamily protein / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBasle, A. / Luis, A.S. / Gilbert, H.J.
CitationJournal: Nat Microbiol / Year: 2018
Title: Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.
Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / ...Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / Venditto, I. / Ralet, M.C. / Henrissat, B. / Martens, E.C. / Mosimann, S.C. / Abbott, D.W. / Gilbert, H.J.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pectate lyase
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3096
Polymers103,1482
Non-polymers1604
Water8,107450
1
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6543
Polymers51,5741
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6543
Polymers51,5741
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.545, 127.545, 263.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Pectate lyase / Galacturonidase


Mass: 51574.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_4155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A066
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium chloride, 100 mM Bis-Tris buffer pH 5.5 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2→48.73 Å / Num. obs: 73408 / % possible obs: 100 % / Redundancy: 26.8 % / CC1/2: 0.998 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 28 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4477 / CC1/2: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
SHELXEmodel building
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→48.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.424 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21534 3667 5 %RANDOM
Rwork0.18171 ---
obs0.18341 69738 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.093 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0 Å20 Å2
2--0.93 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 2→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 4 450 7304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197016
X-RAY DIFFRACTIONr_bond_other_d0.0020.026562
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9589500
X-RAY DIFFRACTIONr_angle_other_deg0.929315230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85324.136324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.777151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1751544
X-RAY DIFFRACTIONr_chiral_restr0.0890.21044
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021428
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_it1.4792.7173458
X-RAY DIFFRACTIONr_mcbond_other1.4752.7163457
X-RAY DIFFRACTIONr_mcangle_it2.2034.0624320
X-RAY DIFFRACTIONr_mcangle_other2.2034.0634321
X-RAY DIFFRACTIONr_scbond_it2.4063.0523558
X-RAY DIFFRACTIONr_scbond_other2.4063.0533559
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.874.4425179
X-RAY DIFFRACTIONr_long_range_B_refined5.331.4017141
X-RAY DIFFRACTIONr_long_range_B_other5.24631.2037080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 273 -
Rwork0.285 5096 -
obs--100 %

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