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- PDB-9d60: Crystal structure of Zn(II)-bound polysaccharide deacetylase from... -

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Basic information

Entry
Database: PDB / ID: 9d60
TitleCrystal structure of Zn(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: 1.36 Å
AuthorsAdamek, O.E. / 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)56,0366
Polymers55,6021
Non-polymers4345
Water9,170509
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.295, 73.112, 95.385
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 41.23 %
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: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→47.69 Å / Num. obs: 1082788 / % possible obs: 96.06 % / Redundancy: 10.8 % / Biso Wilson estimate: 10.75 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.0131 / Net I/σ(I): 35.5
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.1859 / Mean I/σ(I) obs: 11.54 / Num. unique obs: 9259 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.0581 / % possible all: 90.11

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→47.69 Å / SU ML: 0.1093 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1768 1980 1.97 %
Rwork0.165 98393 -
obs0.1653 100373 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.09 Å2
Refinement stepCycle: LAST / Resolution: 1.36→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 25 509 4279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583872
X-RAY DIFFRACTIONf_angle_d0.88195247
X-RAY DIFFRACTIONf_chiral_restr0.0815551
X-RAY DIFFRACTIONf_plane_restr0.0067681
X-RAY DIFFRACTIONf_dihedral_angle_d6.3491522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.22161350.19276422X-RAY DIFFRACTION89.47
1.39-1.430.19231190.18286730X-RAY DIFFRACTION92.45
1.43-1.470.16851440.1716841X-RAY DIFFRACTION94.7
1.47-1.520.18671350.16986923X-RAY DIFFRACTION95.49
1.52-1.580.17671370.16636948X-RAY DIFFRACTION95.52
1.58-1.640.16681380.16136914X-RAY DIFFRACTION95.63
1.64-1.710.19351510.16647028X-RAY DIFFRACTION96.54
1.71-1.80.22521320.17467042X-RAY DIFFRACTION96.71
1.8-1.920.18261450.17147072X-RAY DIFFRACTION97.02
1.92-2.060.1691490.16637135X-RAY DIFFRACTION97.55
2.06-2.270.1681380.1657159X-RAY DIFFRACTION97.38
2.27-2.60.15761540.17017201X-RAY DIFFRACTION98.16
2.6-3.280.17481450.17457353X-RAY DIFFRACTION98.72
3.28-47.690.17451580.1457625X-RAY DIFFRACTION99.26

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