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- PDB-8ew1: Structure of Bacple_01703-E145L -

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Basic information

Entry
Database: PDB / ID: 8ew1
TitleStructure of Bacple_01703-E145L
ComponentsGlycosyl hydrolase family 16
KeywordsHYDROLASE / BACPLE_01703 / glycoside hydrolase of GH16 family
Function / homology
Function and homology information


beta-agarase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Beta-agarase / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / Glycosyl hydrolase family 16
Similarity search - Component
Biological speciesPhocaeicola plebeius DSM 17135 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUlaganathan, T. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biorxiv / Year: 2023
Title: The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations
Authors: Mathieu, S. / Touvrey, M. / Poulet, L. / Drouillard, S. / Ulaganathan, T.S. / Segurel, L. / Cygler, M. / Helbert, W.
History
DepositionOct 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 16
B: Glycosyl hydrolase family 16
C: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,38814
Polymers95,2103
Non-polymers2,17811
Water9,080504
1
A: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5486
Polymers31,7371
Non-polymers8115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4204
Polymers31,7371
Non-polymers6843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4204
Polymers31,7371
Non-polymers6843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.720, 85.720, 112.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Glycosyl hydrolase family 16


Mass: 31736.590 Da / Num. of mol.: 3 / Mutation: E145L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola plebeius DSM 17135 (bacteria)
Gene: BACPLE_01703 / Production host: Escherichia coli (E. coli) / References: UniProt: B5CYA6
#2: Polysaccharide beta-D-galactopyranose-(1-4)-6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 584.501 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4LGalp[6S]a1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1b_1-5][a1221h-1a_1-5_6*OSO/3=O/3=O]/1-2-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-L-Galp6SO3]{[(4+1)][b-D-3-deoxy-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 512 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8K, 0.1 M Hepes pH 7.5 and 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→44.8 Å / Num. obs: 85616 / % possible obs: 98 % / Redundancy: 10 % / CC1/2: 0.99 / Net I/σ(I): 8.35
Reflection shellResolution: 1.8→2 Å / Mean I/σ(I) obs: 3.22 / Num. unique obs: 15141 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EP4

8ep4


Resolution: 1.8→44.8 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 4282 5 %
Rwork0.2271 --
obs0.2285 85616 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 133 504 7215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.62
X-RAY DIFFRACTIONf_dihedral_angle_d12.262546
X-RAY DIFFRACTIONf_chiral_restr0.048924
X-RAY DIFFRACTIONf_plane_restr0.0041223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.38671460.34242769X-RAY DIFFRACTION100
1.82-1.840.30081400.30762664X-RAY DIFFRACTION100
1.84-1.860.32051460.27272777X-RAY DIFFRACTION100
1.86-1.890.29261400.26672665X-RAY DIFFRACTION100
1.89-1.910.2821440.26352724X-RAY DIFFRACTION100
1.91-1.940.32111430.25632727X-RAY DIFFRACTION100
1.94-1.970.27181400.2562652X-RAY DIFFRACTION100
1.97-20.28121460.25272765X-RAY DIFFRACTION100
2-2.030.26271400.23412664X-RAY DIFFRACTION100
2.03-2.060.29161440.22562735X-RAY DIFFRACTION100
2.06-2.10.26561430.24022728X-RAY DIFFRACTION100
2.1-2.130.27171430.23442706X-RAY DIFFRACTION100
2.13-2.180.25771420.23182695X-RAY DIFFRACTION100
2.18-2.220.29241430.22872729X-RAY DIFFRACTION100
2.22-2.270.2441420.22892690X-RAY DIFFRACTION100
2.27-2.320.27651460.21952767X-RAY DIFFRACTION100
2.32-2.380.27411410.22592680X-RAY DIFFRACTION100
2.38-2.440.27271410.22712687X-RAY DIFFRACTION100
2.44-2.510.271440.22972736X-RAY DIFFRACTION100
2.51-2.60.27021420.24132702X-RAY DIFFRACTION100
2.6-2.690.261440.23022726X-RAY DIFFRACTION100
2.69-2.80.26861390.23182650X-RAY DIFFRACTION100
2.8-2.920.24611430.23522710X-RAY DIFFRACTION100
2.92-3.080.23951440.22762740X-RAY DIFFRACTION100
3.08-3.270.23841410.22362666X-RAY DIFFRACTION100
3.27-3.520.25631440.21812734X-RAY DIFFRACTION100
3.52-3.880.22931430.20862723X-RAY DIFFRACTION100
3.88-4.440.22471430.20112721X-RAY DIFFRACTION100
4.44-5.590.24281420.21142693X-RAY DIFFRACTION100
5.6-44.80.24291430.23592709X-RAY DIFFRACTION100

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