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- PDB-7ou9: Crystal structure of dimeric chlorite dismutase variant Q74E (CCl... -

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Basic information

Entry
Database: PDB / ID: 7ou9
TitleCrystal structure of dimeric chlorite dismutase variant Q74E (CCld Q74E) from Cyanothece sp. PCC7425 in complex with nitrite
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Chlorite dismutase / nitrite
Function / homology
Function and homology information


oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / TRIETHYLENE GLYCOL / Chlorite dismutase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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)45,3279
Polymers43,6642
Non-polymers1,6637
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-52 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.697, 52.684, 54.990
Angle α, β, γ (deg.)98.769, 107.105, 109.950
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: 21831.865 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 , 6 types, 107 molecules

#2: 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
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.15 M MgSO4, 23 %w/v PEG 3350, 2 %v/v Glycerol Soaking: 100 mM NaNO2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.42→45.97 Å / Num. obs: 18662 / % possible obs: 96.3 % / Redundancy: 1.7 % / Biso Wilson estimate: 33.51 Å2 / CC1/2: 0.966 / Net I/σ(I): 3.9
Reflection shellResolution: 2.42→2.46 Å / Num. unique obs: 932 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ASB

7asb


Resolution: 2.42→45.97 Å / SU ML: 0.2678 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 953 5.11 %
Rwork0.1815 17700 -
obs0.1843 18653 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.96 Å2
Refinement stepCycle: LAST / Resolution: 2.42→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 113 100 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343209
X-RAY DIFFRACTIONf_angle_d0.5344368
X-RAY DIFFRACTIONf_chiral_restr0.0411443
X-RAY DIFFRACTIONf_plane_restr0.0043556
X-RAY DIFFRACTIONf_dihedral_angle_d10.1905435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.550.27521390.19712490X-RAY DIFFRACTION96.05
2.55-2.710.28011190.20662566X-RAY DIFFRACTION96.03
2.71-2.920.26721440.20012535X-RAY DIFFRACTION95.95
2.92-3.210.27471350.19572519X-RAY DIFFRACTION96.16
3.21-3.680.22711310.17732541X-RAY DIFFRACTION97.2
3.68-4.630.19441450.16222542X-RAY DIFFRACTION96.55
4.63-45.970.23421400.17862507X-RAY DIFFRACTION95.84
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)
15.391493830990.7351946519091.227854340552.73147901282-1.446736807793.92060576765-0.2497828410510.1835613053630.400808926114-0.1211843629810.06262225520030.12041876681-0.559183423815-0.1756825471090.1671178674410.2317999242330.0627033973956-0.002347998992840.229497371916-0.01194750556540.23411600253-17.40759830090.00319716977264-7.82562237978
21.85383693352-0.474974967611-0.2046719703020.7288863125230.460619266033.09542447877-0.08901876656690.0879217527819-0.0980533471360.05208818249830.033689406105-0.08394428918390.170472702410.005465613004740.08660563840830.257550212754-0.02126578810490.00921556438440.232277554795-0.02182753788890.263621752294-7.40404356403-16.4959515125-2.57703560789
31.100963782770.1456074273360.03456030842472.855877295-0.6975232104563.69095321851-0.04986085442010.1426692864020.000554366628501-0.2465488597580.07188650957810.07583492767770.125785318531-0.08640826883120.01118274240750.237246286092-0.0431042761103-0.03214877733980.260766047694-0.03561142735830.292431582868-14.7380859637-14.0841540437-8.12809572411
44.310315653721.499065492720.5001032473793.017251749122.756261796754.18508939286-0.115669537865-0.1479790703290.3479835810330.115951332724-0.128015058650.221157244788-0.647573170846-0.147760893840.1684660450420.344327843243-0.02645354452660.006387429644470.207680839898-0.01027539158420.267602349402-6.601435899853.8784934737926.7603792184
51.84993111261.9550911761.030113423393.570900976181.87835283443.15973748732-0.3328129611590.2370475037650.160390371887-0.4901069335710.235726174570.99659479283-0.5064046320750.02897673539340.1033112494460.2688564194320.0100931008913-0.007998123226170.2921722991040.01373656933780.254820244336-6.8876183903-6.9381892594917.4044418958
61.697180649310.267861188561-0.3856584844182.268358311560.861109226324.039172028980.04182781917980.00266832745484-0.00028678307394-0.033544989968-0.08309636870880.0006789082248670.09700349510130.2404391248990.1057247072160.2058945151930.00945223255467-0.03591428603460.190687732140.0237101885930.235793579392-3.23508332167-16.044814398521.0076803853
72.29346052206-0.172672252209-0.7159983478382.747025244570.3244231966154.177186141840.0515586017923-0.176565716808-0.03295849700510.116098855118-0.0359940815632-0.01179895871460.2533655133880.2541888595330.003543942228310.204126727098-0.0219364696297-0.02693538782240.2357552466310.02734270370750.269965306577-0.25554193575-11.692518985626.5026316206
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 47 )AA2 - 471 - 46
22chain 'A' and (resid 48 through 131 )AA48 - 13147 - 130
33chain 'A' and (resid 132 through 182 )AA132 - 182131 - 181
44chain 'B' and (resid 2 through 47 )BD2 - 471 - 46
55chain 'B' and (resid 48 through 63 )BD48 - 6347 - 62
66chain 'B' and (resid 64 through 108 )BD64 - 10863 - 107
77chain 'B' and (resid 109 through 182 )BD109 - 182108 - 181

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