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- PDB-9d5t: Crystal structure of Cu(II)-bound polysaccharide deacetylase from... -

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Basic information

Entry
Database: PDB / ID: 9d5t
TitleCrystal structure of Cu(II)-bound polysaccharide deacetylase from Bacteroides ovatus
ComponentsPhage tail component domain protein
KeywordsHYDROLASE / esterase
Function / homologyPutative polysaccharide deacetylase / Putative polysaccharide deacetylase / Prokaryotic membrane lipoprotein lipid attachment site profile. / COPPER (II) ION / Phage tail component domain protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYost, O.G. / McLaughlin, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169-01 United States
CitationJournal: Biochemistry / Year: 2025
Title: Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure.
Authors: Schwartz, L.A. / Norman, J.O. / Hasan, S. / Adamek, O.E. / Dzuong, E. / Lowenstein, J.C. / Yost, O.G. / Sankaran, B. / McLaughlin, K.J.
History
DepositionAug 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage tail component domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2188
Polymers55,6021
Non-polymers6167
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.764, 73.183, 95.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phage tail component domain protein


Mass: 55602.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153) (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153
Gene: BACOVA_03992 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAN3A5R0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M NaOAc, 0.1 M Tris pH 8.5, 15% glycerol, 25.5% PEG 4000, [Protein]=16.5 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.56→47.71 Å / Num. obs: 68700 / % possible obs: 99.28 % / Redundancy: 9.6 % / Biso Wilson estimate: 16.23 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.0397 / Net I/σ(I): 15.25
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 10 % / Rmerge(I) obs: 1.119 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 6770 / CC1/2: 0.817 / CC star: 0.948 / Rpim(I) all: 0.367 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Coot1.19.2_4158model building
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→47.71 Å / SU ML: 0.1439 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2005 1993 2.9 %
Rwork0.1746 66676 -
obs0.1754 68669 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.36 Å2
Refinement stepCycle: LAST / Resolution: 1.56→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 37 456 4235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673889
X-RAY DIFFRACTIONf_angle_d0.85265264
X-RAY DIFFRACTIONf_chiral_restr0.0532551
X-RAY DIFFRACTIONf_plane_restr0.0071681
X-RAY DIFFRACTIONf_dihedral_angle_d7.985529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.25771460.22224688X-RAY DIFFRACTION99.36
1.6-1.640.24131320.20194716X-RAY DIFFRACTION99.45
1.64-1.690.25331400.20234700X-RAY DIFFRACTION99.34
1.69-1.750.20571380.20224664X-RAY DIFFRACTION98.6
1.75-1.810.24431610.19684722X-RAY DIFFRACTION99.65
1.81-1.880.2311320.19164785X-RAY DIFFRACTION99.8
1.88-1.970.2011410.1884745X-RAY DIFFRACTION99.84
1.97-2.070.21351420.1754748X-RAY DIFFRACTION99.8
2.07-2.20.19691440.17634764X-RAY DIFFRACTION99.59
2.2-2.370.25081380.18214749X-RAY DIFFRACTION98.89
2.37-2.610.20321400.18124720X-RAY DIFFRACTION97.96
2.61-2.980.23651400.18364812X-RAY DIFFRACTION99.56
2.98-3.760.16991510.1614856X-RAY DIFFRACTION99.68
3.76-47.710.15711480.14925007X-RAY DIFFRACTION98.49

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