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- PDB-9qzk: SadB of Pseudomonas aeruginosa -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9qzk
TitleSadB of Pseudomonas aeruginosa
ComponentsHDOD domain-containing protein
KeywordsSTRUCTURAL PROTEIN / Biofilm / Pseudomonas aeruginosa
Function / homology
Function and homology information


aminoacyl-tRNA deacylase activity / single-species biofilm formation
Similarity search - Function
Uncharacterised conserved protein UCP036888, signal transduction HD-GYP-like, PA5346 type / : / Metal-dependent hydrolase HDOD / HDOD domain / HD-related output (HDOD) domain profile. / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily
Similarity search - Domain/homology
HDOD domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsOpatowsky, Y. / Sporny, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1425/15 Israel
CitationJournal: NPJ Biofilms Microbiomes / Year: 2025
Title: SadB, a mediator of AmrZ proteolysis and biofilm development in Pseudomonas aeruginosa.
Authors: Ben-David, Y. / Sporny, M. / Brochin, Y. / Piscon, B. / Roth, S. / Zander, I. / Nisani, M. / Shoshani, S. / Yaron, O. / Karako-Lampert, S. / Lebenthal-Loinger, I. / Danielli, A. / Opatowsky, Y. / Banin, E.
History
DepositionApr 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HDOD domain-containing protein
B: HDOD domain-containing protein
C: HDOD domain-containing protein
D: HDOD domain-containing protein


Theoretical massNumber of molelcules
Total (without water)201,4754
Polymers201,4754
Non-polymers00
Water00
1
A: HDOD domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,3691
Polymers50,3691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HDOD domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,3691
Polymers50,3691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HDOD domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,3691
Polymers50,3691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HDOD domain-containing protein


Theoretical massNumber of molelcules
Total (without water)50,3691
Polymers50,3691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.727, 162.278, 238.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
HDOD domain-containing protein


Mass: 50368.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5346 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HTL2
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: 5.46 Å3/Da / Density % sol: 77.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Optimal crystal growth conditions consisted of a reservoir content of 1 M ammonium citrate tribasic, pH 7, and 0.1 M Bis-Tris propane, pH 7.25. Crystals were gradually introduced into a cryo- ...Details: Optimal crystal growth conditions consisted of a reservoir content of 1 M ammonium citrate tribasic, pH 7, and 0.1 M Bis-Tris propane, pH 7.25. Crystals were gradually introduced into a cryo-protectant solution consisting of 1.1 M ammonium citrate tribasic, pH 7, 0.1 M Bis-Tris propane, pH 7 and 8% glycerol that was added to the mother-liquor, and flash-frozen in liquid N2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.16→49.25 Å / Num. obs: 75880 / % possible obs: 98.27 % / Redundancy: 6.9 % / CC1/2: 0.994 / Net I/σ(I): 8.82
Reflection shellResolution: 3.164→3.277 Å / Num. unique obs: 6330 / CC1/2: 0.691

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.16→49.25 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 2095 2.81 %
Rwork0.2222 --
obs0.2234 74630 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.16→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14188 0 0 0 14188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614476
X-RAY DIFFRACTIONf_angle_d0.92119720
X-RAY DIFFRACTIONf_dihedral_angle_d4.7232000
X-RAY DIFFRACTIONf_chiral_restr0.0522280
X-RAY DIFFRACTIONf_plane_restr0.0082596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.240.56061070.58163711X-RAY DIFFRACTION77
3.24-3.320.56261400.47494851X-RAY DIFFRACTION100
3.32-3.410.4391400.41574858X-RAY DIFFRACTION100
3.41-3.510.38471400.37334822X-RAY DIFFRACTION100
3.51-3.620.39931400.3284868X-RAY DIFFRACTION100
3.62-3.750.34041400.31464853X-RAY DIFFRACTION100
3.75-3.90.32121410.28864873X-RAY DIFFRACTION100
3.9-4.080.29491400.24564891X-RAY DIFFRACTION100
4.08-4.290.25491410.21734881X-RAY DIFFRACTION100
4.29-4.560.19831420.19454906X-RAY DIFFRACTION100
4.56-4.910.22871420.18864919X-RAY DIFFRACTION100
4.91-5.410.26471430.19594933X-RAY DIFFRACTION100
5.41-6.190.23851430.20964961X-RAY DIFFRACTION100
6.19-7.790.22091450.20095006X-RAY DIFFRACTION100
7.79-49.250.22431510.1635202X-RAY DIFFRACTION100

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