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- PDB-5t3b: Crystal structure of BpGH50 -

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Basic information

Entry
Database: PDB / ID: 5t3b
TitleCrystal structure of BpGH50
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / (alpha/alpha)6 barrel / glycoside hydrolase
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Agarase
Function and homology information
Biological speciesBacteroides plebeius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsGiles, K. / Pluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Proteins / Year: 2017
Title: Structure of a glycoside hydrolase family 50 enzyme from a subfamily that is enriched in human gut microbiome bacteroidetes.
Authors: Giles, K. / Pluvinage, B. / Boraston, A.B.
History
DepositionAug 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 4, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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: Glycoside Hydrolase
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,49720
Polymers109,3802
Non-polymers1,11718
Water17,294960
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A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,55915
Polymers54,6901
Non-polymers86914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9385
Polymers54,6901
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 87.370, 74.670
Angle α, β, γ (deg.)90.000, 105.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycoside Hydrolase


Mass: 54689.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides plebeius (bacteria) / Gene: BACPLE_01683 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5CY86
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 17-25% PEG 3350, 0.04-0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92017 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92017 Å / Relative weight: 1
ReflectionResolution: 1.4→71.95 Å / Num. obs: 176279 / % possible obs: 99.3 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.9 / CC1/2: 0.844 / % possible all: 95.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→71.95 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.538 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1454 8912 5.1 %RANDOM
Rwork0.1056 ---
obs0.1076 167367 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.69 Å2 / Biso mean: 16.817 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.01 Å2
2--0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.4→71.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7354 0 72 960 8386
Biso mean--28.88 30.02 -
Num. residues----915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.028027
X-RAY DIFFRACTIONr_bond_other_d0.0020.027286
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.94510873
X-RAY DIFFRACTIONr_angle_other_deg1.066316875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17651003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44724.747396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.762151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9961529
X-RAY DIFFRACTIONr_chiral_restr0.1270.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021972
X-RAY DIFFRACTIONr_mcbond_it1.7041.3923885
X-RAY DIFFRACTIONr_mcbond_other1.6991.3913884
X-RAY DIFFRACTIONr_mcangle_it2.1032.0994930
X-RAY DIFFRACTIONr_rigid_bond_restr3.102315313
X-RAY DIFFRACTIONr_sphericity_free23.8655597
X-RAY DIFFRACTIONr_sphericity_bonded9.022515445
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 604 -
Rwork0.161 11478 -
all-12082 -
obs--91.8 %

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