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- PDB-7ou5: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -

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Basic information

Entry
Database: PDB / ID: 7ou5
TitleCrystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 in complex with nitrite
ComponentsChlorite Dismutase
KeywordsOXIDOREDUCTASE / Chlorite dismutase / nitrite
Function / homologyHeme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / Chlorite dismutase
Function and homology information
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchmidt, D. / Mlynek, G. / Djinovic-Carugo, K. / Obinger, C.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP30979 Austria
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase.
Authors: Serra, I. / Schmidt, D. / Pfanzagl, V. / Mlynek, G. / Hofbauer, S. / Djinovic-Carugo, K. / Furtmuller, P.G. / Garcia-Rubio, I. / Van Doorslaer, S. / Obinger, C.
History
DepositionJun 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)45,1758
Polymers43,6622
Non-polymers1,5136
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-53 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.749, 52.759, 54.684
Angle α, β, γ (deg.)107.143, 98.829, 109.555
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chlorite Dismutase /


Mass: 21830.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 7425 / ATCC 29141) (bacteria)
Strain: PCC 7425 / ATCC 29141 / Gene: Cyan7425_1434 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8HNS6

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Non-polymers , 5 types, 303 molecules

#2: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.15 M MgSO4, 24 %w/v PEG 3350, 1 %v/v Glycerol Soaking: 50mM NaNO2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.82→46.15 Å / Num. obs: 80245 / % possible obs: 92.15 % / Redundancy: 1.92 % / Biso Wilson estimate: 29.14 Å2 / CC1/2: 0.992 / Net I/σ(I): 5.55
Reflection shellResolution: 1.82→1.93 Å / Num. unique obs: 3670 / CC1/2: 0.597

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MAU

5mau


Resolution: 1.9→33.94 Å / SU ML: 0.2281 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 26.0948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2106 1823 2.6 %
Rwork0.1815 68266 -
obs0.1822 70089 88.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.76 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 103 297 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01073192
X-RAY DIFFRACTIONf_angle_d0.95474349
X-RAY DIFFRACTIONf_chiral_restr0.0557443
X-RAY DIFFRACTIONf_plane_restr0.02553
X-RAY DIFFRACTIONf_dihedral_angle_d11.6304426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.35841440.32125384X-RAY DIFFRACTION91.13
1.95-2.010.31661470.28625428X-RAY DIFFRACTION91.85
2.01-2.070.24981460.25735353X-RAY DIFFRACTION90.89
2.07-2.150.25761400.25115303X-RAY DIFFRACTION90.15
2.15-2.230.26311450.23095302X-RAY DIFFRACTION89.77
2.23-2.340.24111410.2245202X-RAY DIFFRACTION88.28
2.34-2.460.27111370.20695172X-RAY DIFFRACTION87.06
2.46-2.610.26691320.20864960X-RAY DIFFRACTION83.75
2.61-2.810.19511100.18994213X-RAY DIFFRACTION72.12
2.81-3.10.22221410.19475380X-RAY DIFFRACTION90.54
3.1-3.540.18131480.16615621X-RAY DIFFRACTION94.57
3.55-4.460.15961490.13775498X-RAY DIFFRACTION93.77
4.47-33.940.18661430.13945450X-RAY DIFFRACTION92.2
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)
13.020106809140.9884588626861.757784189262.10350165721.538169773294.13158600450.00583337083681-0.08852530049670.207263225236-0.211189741669-0.2533230235770.3943275283360.125063002567-0.7876388567920.1775234720460.282941536799-0.0542952237611-0.01353183820540.370690635726-0.02001833192650.269965640298-5.8814950386-1.072195142693.48260080306
21.930958755280.1636723963691.182087219461.56433478880.542365997925.28514171560.03032558056110.206363282023-0.0417233006387-0.2203984712950.0631339757706-0.1109933365640.2303981823570.462041893775-0.06707310066650.2709473102970.02187731457690.03431722594040.223063345209-0.009949197200630.2505258029849.34726563823-1.421848645493.24903016057
33.154860326140.065381327493-0.4799723828224.72521656495-0.05267587669765.166698431620.0307983855437-0.2378791631570.03918009434460.186768324427-0.2388525389080.354773015099-0.285229454802-1.045478240730.1829056993970.3998241331760.01990893962730.0815124177010.436539752453-0.02506356241990.279889281456-6.377976013810.519843100736.4010306961
42.54556910106-1.14424030999-0.814697077953.83640777119-0.6034600470070.5384381221890.2646922067381.139426567020.0365043505107-0.463522997128-1.206957139041.44841363783-0.111891800374-2.039144533040.7113599944080.4726305604260.0217454585430.02136720052751.13030404994-0.1983487210090.691485123199-14.12473682574.9415385231532.464178362
51.55714180406-0.306017838945-0.4730616151192.032103092060.5331613115655.093517978170.00651457433188-0.03012361603640.01325522363970.2145474674350.0219318291566-0.0563544015185-0.1674137948710.1931163539710.004828214053820.211085067305-0.0351633772332-0.003427093508560.183299463259-0.006457284334330.2037362292418.604588789485.9896771735930.0769444268
62.516632743020.479492656823-0.1859964017942.65600644020.09182307158944.917192512640.152047007255-0.3310182724470.1847052759820.313810803180.0523231656878-0.11420404553-0.6806651107890.462623751328-0.2013965813260.404264557338-0.05181093450690.009242240565040.242878734747-0.06349543737130.2788447579877.9252818195613.226973449738.4685754597
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 63 )AA1 - 631 - 63
22chain 'A' and (resid 64 through 182 )AA64 - 18264 - 182
33chain 'B' and (resid 1 through 32 )BE1 - 321 - 32
44chain 'B' and (resid 33 through 47 )BE33 - 4733 - 47
55chain 'B' and (resid 48 through 148 )BE48 - 14848 - 148
66chain 'B' and (resid 149 through 182 )BE149 - 182149 - 182

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