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- PDB-5ta1: Crystal structure of BuGH86wt -

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Basic information

Entry
Database: PDB / ID: 5ta1
TitleCrystal structure of BuGH86wt
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase
Function / homology
Function and homology information


Jelly Rolls - #1200 / Porphyranase catalytic subdomain 1 / Beta-porphyranase A, C-terminal / beta porphyranase A C-terminal / Porphyranase beta-sandwich domain 1 / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,33311
Polymers74,7491
Non-polymers58510
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-9 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.660, 167.660, 167.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1010-

HOH

21A-1058-

HOH

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Components

#1: Protein Glycoside Hydrolase


Mass: 74748.672 Da / Num. of mol.: 1
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: A0A2D0TCD3*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M CaOAc, 0.08 M Na cacodylate, 14.4% PEG 3350, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→118.55 Å / Num. obs: 34836 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.7 / CC1/2: 0.916 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AW7

4aw7


Resolution: 2.3→118.55 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.053 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 1750 5 %RANDOM
Rwork0.1684 ---
obs0.1706 33085 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.32 Å2 / Biso mean: 42.831 Å2 / Biso min: 22.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.3→118.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5051 0 33 261 5345
Biso mean--52.82 42.21 -
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195211
X-RAY DIFFRACTIONr_bond_other_d0.0020.024814
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9497043
X-RAY DIFFRACTIONr_angle_other_deg0.915311084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96224.504262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34415878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6671527
X-RAY DIFFRACTIONr_chiral_restr0.0780.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021240
X-RAY DIFFRACTIONr_mcbond_it2.2274.1852517
X-RAY DIFFRACTIONr_mcbond_other2.2264.1842516
X-RAY DIFFRACTIONr_mcangle_it3.3726.2693148
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 143 -
Rwork0.221 2399 -
all-2542 -
obs--100 %

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