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- PDB-9d44: Crystal structure of Co(II)-bound polysaccharide deacetylase from... -

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Basic information

Entry
Database: PDB / ID: 9d44
TitleCrystal structure of Co(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. / metal ion binding / : / Phage tail component domain protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsLowenstein, J.C. / 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 12, 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)56,2148
Polymers55,6021
Non-polymers6117
Water8,935496
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)69.177, 73.162, 95.424
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
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, 27% 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: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→44.47 Å / Num. obs: 91845 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 12.79 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1118 / Rpim(I) all: 0.039 / Net I/σ(I): 16.37
Reflection shellResolution: 1.42→1.471 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.342 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 9050 / CC1/2: 0.807 / CC star: 0.945 / Rpim(I) all: 0.463 / % possible all: 100

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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: 1.42→44.47 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 1996 2.17 %
Rwork0.1599 89815 -
obs0.1607 91811 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.72 Å2
Refinement stepCycle: LAST / Resolution: 1.42→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 37 496 4275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493875
X-RAY DIFFRACTIONf_angle_d0.77585246
X-RAY DIFFRACTIONf_chiral_restr0.0776550
X-RAY DIFFRACTIONf_plane_restr0.0059679
X-RAY DIFFRACTIONf_dihedral_angle_d12.55051429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.28641400.22446313X-RAY DIFFRACTION100
1.46-1.490.3171450.22416344X-RAY DIFFRACTION99.98
1.49-1.540.29211420.22026357X-RAY DIFFRACTION99.98
1.54-1.590.27691290.18446356X-RAY DIFFRACTION99.97
1.59-1.650.21441510.15316359X-RAY DIFFRACTION99.94
1.65-1.710.17651340.14256367X-RAY DIFFRACTION99.95
1.71-1.790.18941370.14986373X-RAY DIFFRACTION99.97
1.79-1.880.22261470.1576377X-RAY DIFFRACTION99.95
1.88-20.18821440.14636400X-RAY DIFFRACTION99.95
2-2.160.21291410.14976428X-RAY DIFFRACTION99.95
2.16-2.370.18681430.15266417X-RAY DIFFRACTION99.89
2.37-2.720.20261440.1666468X-RAY DIFFRACTION99.82
2.72-3.420.18221470.16336506X-RAY DIFFRACTION99.89

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