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- PDB-9d4i: Crystal structure of Ni(II)-bound polysaccharide deacetylase from... -

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Basic information

Entry
Database: PDB / ID: 9d4i
TitleCrystal structure of Ni(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. / NICKEL (II) ION / Phage tail component domain protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsDzuong, 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 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)56,0296
Polymers55,6021
Non-polymers4275
Water11,692649
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)68.945, 73.041, 95.163
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 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: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→47.58 Å / Num. obs: 80482 / % possible obs: 99.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 15.43 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0722 / Rpim(I) all: 0.0263 / Net I/σ(I): 19.95
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 68163 / CC1/2: 0.778 / CC star: 0.936 / Rpim(I) all: 0.35 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→47.58 Å / SU ML: 0.1609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1931 1996 2.48 %
Rwork0.1663 78463 -
obs0.167 80459 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.02 Å2
Refinement stepCycle: LAST / Resolution: 1.48→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 25 649 4419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543890
X-RAY DIFFRACTIONf_angle_d0.82475273
X-RAY DIFFRACTIONf_chiral_restr0.0789553
X-RAY DIFFRACTIONf_plane_restr0.007685
X-RAY DIFFRACTIONf_dihedral_angle_d13.20081444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.31491430.29345517X-RAY DIFFRACTION99.39
1.52-1.560.24391310.23875532X-RAY DIFFRACTION99.4
1.56-1.60.2291540.19015508X-RAY DIFFRACTION99.39
1.6-1.660.22181330.18275534X-RAY DIFFRACTION99.75
1.66-1.710.241510.1845548X-RAY DIFFRACTION99.84
1.71-1.780.21071340.19465581X-RAY DIFFRACTION99.79
1.78-1.860.20741340.17775611X-RAY DIFFRACTION99.9
1.86-1.960.20911480.17395524X-RAY DIFFRACTION99.47
1.96-2.090.18411440.16315590X-RAY DIFFRACTION99.67
2.09-2.250.18771400.16125585X-RAY DIFFRACTION99.88
2.25-2.470.21481480.16635629X-RAY DIFFRACTION99.86
2.47-2.830.20191430.16525661X-RAY DIFFRACTION99.83
2.83-3.570.17381450.15265718X-RAY DIFFRACTION99.85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.002347574130220.002105960475310.001407603736040.001082412698890.001862548664190.00259837868677-0.001253131817760.000314574988010.00252134501686-0.000152002521842-0.0008055697545840.001687500006870.002844680016340.007058339501573.51561251337E-80.04730753811710.0106235391396-0.000231549544570.0497842130017-0.0005503691573160.057450505951316.50096410182.341668612358.6944714856
2-0.00134804228361-0.00286131904536-0.000539709045101-0.0004273318279377.88487813121E-59.68304830303E-5-0.00387999120245-0.007553131527710.00512099708155-0.00193216269830.006214996724040.00626407996123-0.00695742680575-0.0116426972376-2.98522053834E-9-0.03298466163820.04871201016190.0180579361562-0.0466222635281-0.0123575969739-0.0223677533995-3.8217612788910.96453819019.56190834553
30.00223372053613-0.0002418260934310.00210149584390.0003037273996640.001336508346050.002563465561270.007981243416090.00214335833391-0.0121592638757-0.00923515044793-0.003869478390090.00560775044756-0.00201961707226-0.00853565617213-9.26980388729E-90.0471349807264-0.0105442258872-0.003052202153840.04542323908690.001613967157430.0380926764956-4.86584939823-4.15295386365-4.2535961797
40.00456467948196-0.003203334606450.002985754359230.00238736740727-0.004119078339950.00396286006091-0.00993756339071-0.0227789515980.001301398724020.00382560428480.01338363748-0.002527007333510.002644527124910.003404079302552.21734086096E-100.0345219842649-0.003653995052150.004649515521040.03856806396520.002116708039720.039363498355613.6957156459-2.3637654588512.1254697497
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 40 through 88 )40 - 881 - 49
22chain 'A' and (resid 89 through 212 )89 - 21250 - 173
33chain 'A' and (resid 213 through 323 )213 - 323174 - 284
44chain 'A' and (resid 324 through 499 )324 - 499285 - 460

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