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- PDB-5t9x: Crystal structure of BuGH16Bwt -

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Basic information

Entry
Database: PDB / ID: 5t9x
TitleCrystal structure of BuGH16Bwt
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase
Function / homology
Function and homology information


beta-agarase activity / carbohydrate metabolic process
Similarity search - Function
Beta-agarase / : / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Glycoside Hydrolase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsPluvinage, B. / Boraston, A.B.
CitationJournal: Nat Commun / Year: 2018
Title: Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont.
Authors: Pluvinage, B. / Grondin, J.M. / Amundsen, C. / Klassen, L. / Moote, P.E. / Xiao, Y. / Thomas, D. / Pudlo, N.A. / Anele, A. / Martens, E.C. / Inglis, G.D. / Uwiera, R.E.R. / Boraston, A.B. / Abbott, D.W.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside Hydrolase
B: Glycoside Hydrolase
C: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6339
Polymers117,3573
Non-polymers2766
Water7,098394
1
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2113
Polymers39,1191
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2113
Polymers39,1191
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2113
Polymers39,1191
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.070, 109.070, 239.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycoside Hydrolase


Mass: 39118.957 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: NP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCD1*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M NaCl, 0.1 M imidazole-HCl, 0.4 M NaH2PO4/1.6 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.28215 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28215 Å / Relative weight: 1
ReflectionResolution: 2.5→99.25 Å / Num. obs: 50683 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.721 / % possible all: 100

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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
Starting model: 4AWD

4awd


Resolution: 2.5→99.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.908 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.209
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 2469 4.9 %RANDOM
Rwork0.1661 ---
obs0.1681 48136 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.2 Å2 / Biso mean: 31.203 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.5→99.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7211 0 18 394 7623
Biso mean--44.03 30.28 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197423
X-RAY DIFFRACTIONr_bond_other_d0.0020.026605
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9210089
X-RAY DIFFRACTIONr_angle_other_deg0.988315237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9615886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17924.392378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.984151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6911539
X-RAY DIFFRACTIONr_chiral_restr0.0940.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021781
X-RAY DIFFRACTIONr_mcbond_it2.0483.0163553
X-RAY DIFFRACTIONr_mcbond_other2.0483.0153552
X-RAY DIFFRACTIONr_mcangle_it3.3854.5144436
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 201 -
Rwork0.249 3492 -
all-3693 -
obs--99.97 %

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