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- PDB-8ep4: Structure of Bacple_01703 -

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Basic information

Entry
Database: PDB / ID: 8ep4
TitleStructure of Bacple_01703
ComponentsGlycosyl hydrolase family 16
KeywordsHYDROLASE / BACPLE_01703 / glycoside hydrolase of GH16 family
Function / homology
Function and homology information


beta-agarase activity / carbohydrate metabolic process
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 / DI(HYDROXYETHYL)ETHER / Glycosyl hydrolase family 16
Similarity search - Component
Biological speciesPhocaeicola plebeius DSM 17135 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: 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.title / _citation.year
Revision 1.2Oct 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)96,59317
Polymers95,2583
Non-polymers1,33614
Water13,511750
1
A: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1495
Polymers31,7531
Non-polymers3964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3548
Polymers31,7531
Non-polymers6027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0904
Polymers31,7531
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.330, 85.330, 112.910
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 , 1 types, 3 molecules ABC

#1: Protein Glycosyl hydrolase family 16


Mass: 31752.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola plebeius DSM 17135 (bacteria)
Strain: DSM 17135 / JCM 12973 / M2 / Gene: BACPLE_01703 / Production host: Escherichia coli (E. coli) / References: UniProt: B5CYA6

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Non-polymers , 5 types, 764 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 750 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 16% Peg 8K, 0.1 M Hepes pH 7.5 and 0.2M 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: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 68053 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.99 / Net I/σ(I): 10.76
Reflection shellResolution: 1.94→2.05 Å / Mean I/σ(I) obs: 2.35 / Num. unique obs: 10371 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUU

3juu


Resolution: 1.94→44.86 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2.13 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 3402 5 %
Rwork0.1559 --
obs0.1577 68040 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 80 750 7458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076956
X-RAY DIFFRACTIONf_angle_d0.8339447
X-RAY DIFFRACTIONf_dihedral_angle_d13.0722509
X-RAY DIFFRACTIONf_chiral_restr0.062883
X-RAY DIFFRACTIONf_plane_restr0.0071239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.31151420.27272690X-RAY DIFFRACTION100
1.97-20.31221440.24562743X-RAY DIFFRACTION100
2-2.030.23851390.2222650X-RAY DIFFRACTION100
2.03-2.060.25241420.20482684X-RAY DIFFRACTION100
2.06-2.10.25671410.19312677X-RAY DIFFRACTION100
2.1-2.140.24021440.18692747X-RAY DIFFRACTION100
2.14-2.180.22631420.1742695X-RAY DIFFRACTION100
2.18-2.220.24521400.16792657X-RAY DIFFRACTION100
2.22-2.270.21091400.17032668X-RAY DIFFRACTION100
2.27-2.320.23691430.17462701X-RAY DIFFRACTION100
2.32-2.380.20431440.17062741X-RAY DIFFRACTION100
2.38-2.440.20941400.1522653X-RAY DIFFRACTION100
2.44-2.520.20531430.1552718X-RAY DIFFRACTION100
2.52-2.60.22031410.1642686X-RAY DIFFRACTION100
2.6-2.690.1941410.15382699X-RAY DIFFRACTION100
2.69-2.80.19781410.15362672X-RAY DIFFRACTION100
2.8-2.920.17991420.15362707X-RAY DIFFRACTION100
2.93-3.080.19881420.1492696X-RAY DIFFRACTION100
3.08-3.270.16451420.1412691X-RAY DIFFRACTION100
3.27-3.520.17481420.13932693X-RAY DIFFRACTION100
3.53-3.880.15181420.13392708X-RAY DIFFRACTION100
3.88-4.440.14531410.12092686X-RAY DIFFRACTION100
4.44-5.590.16351420.13622687X-RAY DIFFRACTION100
5.6-44.860.19761420.17032689X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4810.0452-0.14530.71440.00721.4129-0.0183-0.00690.0074-0.05060.01720.00690.0275-0.00930.00270.106-0.0101-0.00410.1266-0.00450.137839.0334-19.2252-22.0236
20.3343-0.0550.15350.747-0.07391.49390.01150.0065-0.01450.05270.00310.0247-0.0365-0.0116-0.01440.11340.01030.0010.1436-0.00270.158539.05419.18771.017
30.93780.0757-0.00191.0191-0.21661.8308-0.04740.0534-0.0824-0.0150.07130.0709-0.0434-0.0728-0.0190.2405-0.0007-0.00150.2554-0.01640.242280.5445-4.49950.1067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 267)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 267)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 266)

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