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- PDB-7ou7: Crystal structure of dimeric chlorite dismutase variant Q74V (CCl... -

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Basic information

Entry
Database: PDB / ID: 7ou7
TitleCrystal structure of dimeric chlorite dismutase variant Q74V (CCld Q74V) from Cyanothece sp. PCC7425 in complex with nitrite
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Chlorite dismutase / nitrite
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / 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 / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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

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Assembly

Deposited unit
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0217
Polymers43,6042
Non-polymers1,4175
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-43 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.954, 73.049, 59.973
Angle α, β, γ (deg.)90.000, 112.323, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Chlorite dismutase


Mass: 21801.883 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
#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-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 %w/v PEG 8K, 0.1 M TRIS pH 8.5, 0.2 M MgCl2 Soaking: 100mM 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: 1.4→47.54 Å / Num. obs: 52809 / % possible obs: 76.2 % / Redundancy: 1.29 % / Biso Wilson estimate: 22.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 7.96
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 5233 / CC1/2: 0.174

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ATI

7ati


Resolution: 1.63→47.54 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1888 851 1.61 %
Rwork0.1676 51924 -
obs0.1679 52775 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.19 Å2
Refinement stepCycle: LAST / Resolution: 1.63→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 98 231 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583191
X-RAY DIFFRACTIONf_angle_d0.76334350
X-RAY DIFFRACTIONf_chiral_restr0.0545446
X-RAY DIFFRACTIONf_plane_restr0.0081553
X-RAY DIFFRACTIONf_dihedral_angle_d11.5616428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.730.31561410.26958591X-RAY DIFFRACTION95.84
1.73-1.870.27111400.19838520X-RAY DIFFRACTION95.87
1.87-2.050.17391390.17158569X-RAY DIFFRACTION95.63
2.05-2.350.19441420.15488634X-RAY DIFFRACTION96.25
2.35-2.960.17831430.16778762X-RAY DIFFRACTION97.5
2.96-47.540.17191460.15678848X-RAY DIFFRACTION97.26
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)
10.282847594575-0.01576042422190.07958773325560.4503038956370.5148732153340.5359714275760.04353448746460.1371957704650.1112161909390.00546167820346-0.208777837833-0.0769144244801-0.1913606343620.206824586073-0.000137996750090.266290972204-0.0367419221393-0.004453482919310.2683248538530.03150658459220.28450262802234.29454404797.2886235090417.7868028172
22.10338667831-0.1653008901210.4810326194350.746385016512-0.2496409401811.34878995855-0.0103268348391-0.194635470904-0.03110727451270.0457939434939-0.0509369076386-0.00963138173901-0.0281517062842-0.0236056872977-0.0003286718555960.188180621724-0.01445075574970.01355184838130.208468998220.01502728435160.17421987076221.7850407756-0.84063824762723.0076960942
30.450197082135-0.08329071877140.5948596719111.298146135360.2108770610921.43350903628-0.074634486008-0.298090048996-0.1973555298560.1473872069620.0535264724253-0.08433875199190.07761087923190.118633534343-4.35916554229E-50.239498562233-0.000752897518725-0.004952245451510.2975491394940.05195343214960.19944244060929.3950927847-5.2750248216428.8642665944
42.159305898180.2815348916040.2054448404221.39209631042-0.1317901621571.299677587360.001807857854240.144724073096-0.0638553575969-0.135180688290.03618490152140.07871960025580.185505921551-0.1473006381340.0005590733306120.239205786959-0.040833481314-0.007898119979040.169122729112-0.0007991862848630.147347088761.45239759235-3.88419429951-6.05469081537
50.761376783598-0.2371765913060.9319994383791.6460132585-1.283792827511.75407741448-0.196767227110.690524337798-0.727914866689-0.505351119301-0.523581498107-0.5690118898260.5842300359520.431566738296-0.2240424621050.4104660613250.04570261180340.1158911183520.485275629507-0.06213149854960.4080992391518.44620305203-12.7804767769-6.83468358036
60.6300500602890.2874251163080.3079146784050.538126136943-0.2810753539070.5275906496730.0125468396885-0.0369911640035-0.0135383106329-0.01794136565310.001755882393010.03138618856870.148650879412-0.131842054645-3.27611673728E-50.1911134469380.00144116250458-0.00334406794150.194876230386-0.01227447055090.1608742243468.61546059702-0.4076012945737.64632137297
70.4590420546290.0315351005330.228776886390.007922402033910.06480814953720.5555599727410.26114228389-0.246464028956-0.4445677078910.01650996522980.208683428164-0.3653579610180.457151603424-0.6648533633470.025826937960.304584782687-0.0190074264952-0.01980899696960.424635981502-0.0005508295020730.28223821052-2.344609506296.6373290523320.4705093655
80.507322955871-0.3048117339340.4065115555160.7951021840540.3569597598391.89150387392-0.01596629071380.0741134091128-0.0139804751921-0.007594355151790.04274659756-0.009178266590180.0373402724277-0.083887974290.0001240049578840.1574727987590.01391740833830.00496158425460.1367409147030.02095733816220.1597659640852.763331621594.57196951884.07426727752
90.17838045371-0.1148900435480.1099335700150.2247695228570.007289739684620.0808255468922-0.108435472009-0.1404544022060.2324711520690.2437620504140.07426827006490.100470460453-0.3225297782180.0480409603058-0.0001859195506560.2761900982440.0255603530527-0.008086248379230.163606252048-0.02778572447090.257335690749.9914449019616.749175949813.7572090641
100.114954856928-0.03294750860260.007117525326340.00870296730521-0.01711656353260.05294858526-0.0423380105985-0.06332222432250.188472479354-0.128695429317-0.11678872215-0.0154356083974-0.318869730478-0.4700955161680.0002359664252380.2138177154760.03667194552240.0055069322120.261729074216-0.01832183740920.265365678108-5.0822872870812.075814915710.5661172391
110.340809548330.1135324756760.1045486262410.759779255541-0.06137861809060.404777571336-0.0694480494210.244254031132-0.0697763170581-0.04086768509910.0515547143368-0.0520591075520.110845977842-0.151574899709-9.49345701859E-50.194878478822-0.00178345563060.003744579861970.2117316072670.0007330059887490.1848932056218.709818155030.3169139847284.1166138273
120.0073059680308-0.009630136899460.1285746309180.835338591287-0.2788321748451.07923826377-0.1299157903770.02465462631030.0967954819885-0.1883283120380.1599361666990.300177210102-0.158776810558-0.2879069774790.0002899214808180.1980559976530.0175624947799-0.02478105122150.2092048411490.01898780672660.265032252569-4.851736402989.105141327311.41282814543
130.37548136957-0.424982932432-0.09806360858671.01671503931-0.3208457316691.3411961274-0.07426263855270.1897598273280.0616842978887-0.04417247940840.1240617794870.00510671499961-0.0865644515959-0.0694491806259-0.0006904125611690.202263965625-0.00610559498210.02209056955990.1883369756160.01639002646950.2042980562813.254373611848.17529257409-1.96222925267
142.026395668410.464445530810.05211988493150.8508344346920.4592336858960.9290086646740.117569211954-0.0138893645483-0.427887489496-0.0252622618705-0.0435565096399-0.2452201479910.3039646253120.249759457506-4.51720064231E-50.2890228447350.07230306606410.02540091649710.2136198898020.05947017891310.30837934007331.0593948475-15.383563596617.3152629049
151.74908450579-0.06833757801820.485294047631.02889897208-0.7151804779851.684923771770.1662295454180.122327678975-0.490346928076-0.379584616635-0.161054180728-0.06465619054640.4530210273930.09353988283530.03020090902220.3016754787720.0231377218417-0.008340112515280.159484083613-0.0007080379445840.2974955809523.5013675894-10.20324713912.0410360714
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 64 through 83 )BD64 - 8364 - 83
22chain 'B' and (resid 84 through 148 )BD84 - 14884 - 148
33chain 'B' and (resid 149 through 182 )BD149 - 182149 - 182
44chain 'A' and (resid 1 through 37 )AA1 - 371 - 37
55chain 'A' and (resid 38 through 49 )AA38 - 4938 - 49
66chain 'A' and (resid 50 through 63 )AA50 - 6350 - 63
77chain 'A' and (resid 64 through 73 )AA64 - 7364 - 73
88chain 'A' and (resid 74 through 100 )AA74 - 10074 - 100
99chain 'A' and (resid 101 through 113 )AA101 - 113101 - 113
1010chain 'A' and (resid 114 through 124 )AA114 - 124114 - 124
1111chain 'A' and (resid 125 through 140 )AA125 - 140125 - 140
1212chain 'A' and (resid 141 through 164 )AA141 - 164141 - 164
1313chain 'A' and (resid 165 through 182 )AA165 - 182165 - 182
1414chain 'B' and (resid 1 through 37 )BD1 - 371 - 37
1515chain 'B' and (resid 38 through 63 )BD38 - 6338 - 63

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