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- PDB-9g8t: Crystal structure of the persulfide dioxygenase (PDO - PA2915) fr... -

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Basic information

Entry
Database: PDB / ID: 9g8t
TitleCrystal structure of the persulfide dioxygenase (PDO - PA2915) from Pseudomonas aeruginosa
ComponentsMetallo-beta-lactamase domain-containing protein
KeywordsOXIDOREDUCTASE / Persulfide / GSH / GSSH / Nitric oxide / beta-lactamase MBL
Function / homology
Function and homology information


hydrogen sulfide metabolic process / sulfur dioxygenase activity / glutathione metabolic process / metal ion binding
Similarity search - Function
Persulfide dioxygenase-like, MBL-fold metallo-hydrolase domain / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Metallo-beta-lactamase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsTroilo, F. / Giordano, F. / Giuffre, A. / Giardina, G. / Di Matteo, A.
Funding supportEuropean Union, Italy, 3items
OrganizationGrant numberCountry
European Union (EU)PE00000007European Union
Ministero dell Universita e della Ricerca20224BYR59 Italy
European Union (EU)IR0000009European Union
CitationJournal: To Be Published
Title: Crystal structure of the persulfide dioxygenase (PDO - PA2915) from Pseudomonas aeruginosa
Authors: Troilo, F. / Giordano, F. / Forte, E. / Giardina, G. / Travaglini-Allocatelli, C. / Giuffre, A. / Di Matteo, A.
History
DepositionJul 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3675
Polymers33,1241
Non-polymers2424
Water1,40578
1
A: Metallo-beta-lactamase domain-containing protein
hetero molecules

A: Metallo-beta-lactamase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,73410
Polymers66,2492
Non-polymers4858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3630 Å2
ΔGint-107 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.240, 77.240, 83.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

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Components

#1: Protein Metallo-beta-lactamase domain-containing protein


Mass: 33124.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2915 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZT2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.17 Å3/Da / Density % sol: 45 % / Description: rod-like crystals 30x30x150 micron
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 microL of protein solution (8 mg/mL) with 1 microL of the reservoir solution (Morpheus Molecular dimension A9) containing: 0.06 M Divalents (0.03 M Magnesium chloride hexahydrate; 0.03 M ...Details: 1.5 microL of protein solution (8 mg/mL) with 1 microL of the reservoir solution (Morpheus Molecular dimension A9) containing: 0.06 M Divalents (0.03 M Magnesium chloride hexahydrate; 0.03 M Calcium chloride dihydrate); 0.1 M Buffer System 3 pH 8.5 (0.05 M Tris (base); 0.05 M BICINE); 30% v/v Precipitant Mix 1 (20% v/v PEG 500 MME; 10% w/v PEG 20000) and equilibrated versus 500 microL of reservoir solution
Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2022
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→66.89 Å / Num. obs: 18119 / % possible obs: 100 % / Redundancy: 17.51 % / Biso Wilson estimate: 45.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.022 / Net I/σ(I): 18.16
Reflection shellResolution: 2.063→2.099 Å / Rmerge(I) obs: 1.741 / Mean I/σ(I) obs: 2.212 / Num. unique obs: 888 / CC1/2: 0.8554 / Rpim(I) all: 0.423

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
XSCALE20220120data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→66.89 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 921 5.09 %
Rwork0.192 --
obs0.1944 18096 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→66.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 10 78 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082257
X-RAY DIFFRACTIONf_angle_d0.913062
X-RAY DIFFRACTIONf_dihedral_angle_d16.278317
X-RAY DIFFRACTIONf_chiral_restr0.055332
X-RAY DIFFRACTIONf_plane_restr0.007410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.170.29941340.25562387X-RAY DIFFRACTION100
2.17-2.310.33661120.24982439X-RAY DIFFRACTION100
2.31-2.490.31931240.23112439X-RAY DIFFRACTION100
2.49-2.740.26761320.22452416X-RAY DIFFRACTION100
2.74-3.130.26391380.22252440X-RAY DIFFRACTION100
3.13-3.950.2221370.19642484X-RAY DIFFRACTION100
3.95-66.890.21441440.16012570X-RAY DIFFRACTION100
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)
11.15440.1194-0.64991.23150.82770.9901-0.0444-0.14830.13970.18530.2372-0.1006-0.31210.33930.00210.60270.1364-0.07570.2968-0.05860.405630.743112.6545.1322
20.79650.27650.3922.35320.34681.9254-0.1933-0.1499-0.07140.60030.15660.10530.3116-0.14380.00060.62580.11460.02780.2919-0.0010.394723.3927-0.35657.9449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 135 )
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 288 )

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