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- PDB-9gtj: Chlorite dismutase from Pseudomonas sp. -

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Basic information

Entry
Database: PDB / ID: 9gtj
TitleChlorite dismutase from Pseudomonas sp.
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Chlorite degradation / Metagenomics / Soil / Bioremediation / Heme
Function / homologyHeme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Chlorite dismutase
Function and homology information
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsPapageorgiou, A.C. / Chronopoulou, E.G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-DiscoveryEuropean Union
CitationJournal: Febs J. / Year: 2025
Title: Biochemical and structural characterization of chlorite dismutase enzyme from Pseudomonas aeruginosa.
Authors: Nokas, D.V. / Panagiotopoulou, E.K. / Kapogiannatos, A.I. / Premetis, G.E. / Labrou, N.E. / Efthimiadou, E.K. / Papageorgiou, A.C. / Chronopoulou, E.G.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,77313
Polymers44,2282
Non-polymers1,54511
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-122 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.460, 45.971, 90.156
Angle α, β, γ (deg.)90.00, 129.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chlorite dismutase


Mass: 22114.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Gene: SAMN05216605_1413 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G8UKZ8

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Non-polymers , 5 types, 752 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.77 % / Description: Rods
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.2M Ammonium citrate dibasic; 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.99→49.32 Å / Num. obs: 217930 / % possible obs: 97.2 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 14.8 / Num. measured all: 1488111
Reflection shellResolution: 0.99→1.02 Å / % possible obs: 92.6 % / Redundancy: 7 % / Rmerge(I) obs: 2.346 / Num. measured all: 141992 / Num. unique obs: 20381 / CC1/2: 0.364 / Rpim(I) all: 0.944 / Rrim(I) all: 2.532 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.99→49.32 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.702 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16067 2000 -RANDOM
Rwork0.1435 ---
obs0.14365 215927 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0.03 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 0.99→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 103 741 3822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123224
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163032
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.7024422
X-RAY DIFFRACTIONr_angle_other_deg0.6361.5866878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3085387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.898538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72710513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023911
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02837
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7722.51498
X-RAY DIFFRACTIONr_mcbond_other2.7732.8641498
X-RAY DIFFRACTIONr_mcangle_it2.92375.0211874
X-RAY DIFFRACTIONr_mcangle_other2.92575.3061875
X-RAY DIFFRACTIONr_scbond_it1.5121.5121726
X-RAY DIFFRACTIONr_scbond_other1.5121727
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0632539
X-RAY DIFFRACTIONr_long_range_B_refined3.9834110
X-RAY DIFFRACTIONr_long_range_B_other2.8273746
X-RAY DIFFRACTIONr_rigid_bond_restr8.42433217
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 141 -
Rwork0.326 15122 -
obs--92.36 %

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