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- PDB-8zbd: Crystal structure of Persulfide Dioxygenase from Beggiatoa leptom... -

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Basic information

Entry
Database: PDB / ID: 8zbd
TitleCrystal structure of Persulfide Dioxygenase from Beggiatoa leptomitoformis
ComponentsMBL fold metallo-hydrolase
KeywordsOXIDOREDUCTASE / Beggiatoa / persulfide dioxygenase / oxidation of intracellular elemental sulfur / thiosulphate
Function / homology
Function and homology information


hydrogen sulfide metabolic process / sulfur dioxygenase activity / glutathione metabolic process / hydrolase activity
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
: / MBL fold metallo-hydrolase
Similarity search - Component
Biological speciesBeggiatoa leptomitoformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Rudenko, T.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2024
Title: Mechanism of Intracellular Elemental Sulfur Oxidation in Beggiatoa leptomitoformis , Where Persulfide Dioxygenase Plays a Key Role.
Authors: Rudenko, T.S. / Trubitsina, L.I. / Terentyev, V.V. / Trubitsin, I.V. / Borshchevskiy, V.I. / Tishchenko, S.V. / Gabdulkhakov, A.G. / Leontievsky, A.A. / Grabovich, M.Y.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MBL fold metallo-hydrolase
B: MBL fold metallo-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2844
Polymers55,1732
Non-polymers1122
Water1,78399
1
A: MBL fold metallo-hydrolase
hetero molecules

B: MBL fold metallo-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2844
Polymers55,1732
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z+1/41
Buried area2280 Å2
ΔGint-37 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.997, 66.997, 245.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein MBL fold metallo-hydrolase


Mass: 27586.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beggiatoa leptomitoformis (bacteria) / Gene: BLE401_10280 / Plasmid: pET-22b(+) / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: A0A2N9YEY8
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10mg/ml, 8% w/v PEG 4000, 0.2M imidazole malate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 24873 / % possible obs: 99.6 % / Redundancy: 10 % / Biso Wilson estimate: 32.34 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.27 / Net I/σ(I): 10.13
Reflection shellResolution: 2.33→2.47 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3845 / CC1/2: 0.71 / Rrim(I) all: 1.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→46.51 Å / SU ML: 0.3102 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246 1205 4.85 %
Rwork0.1892 23629 -
obs0.192 24834 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.88 Å2
Refinement stepCycle: LAST / Resolution: 2.33→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 2 99 3745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793728
X-RAY DIFFRACTIONf_angle_d0.98435068
X-RAY DIFFRACTIONf_chiral_restr0.0545574
X-RAY DIFFRACTIONf_plane_restr0.008662
X-RAY DIFFRACTIONf_dihedral_angle_d6.4139506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.420.33191290.26622491X-RAY DIFFRACTION97.33
2.42-2.530.36131260.26762574X-RAY DIFFRACTION100
2.53-2.670.36071210.25142589X-RAY DIFFRACTION100
2.67-2.830.31981250.22152586X-RAY DIFFRACTION99.85
2.83-3.050.26751360.21952622X-RAY DIFFRACTION99.93
3.05-3.360.27371360.20212594X-RAY DIFFRACTION99.93
3.36-3.850.25361590.17292614X-RAY DIFFRACTION100
3.85-4.840.17261250.14082704X-RAY DIFFRACTION100
4.84-46.510.18271480.16062855X-RAY DIFFRACTION99.8

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