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- PDB-7oua: Crystal structure of dimeric chlorite dismutase variant R127K (CC... -

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Basic information

Entry
Database: PDB / ID: 7oua
TitleCrystal structure of dimeric chlorite dismutase variant R127K (CCld R127K) from Cyanothece sp. PCC7425
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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chlorite dismutase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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)45,97412
Polymers43,6062
Non-polymers2,36810
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-28 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.712, 49.607, 54.579
Angle α, β, γ (deg.)102.484, 104.838, 105.002
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: 21802.867 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 , 7 types, 42 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.15 M MgSO4, 30 %w/v PEG 3350, 4 %v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→50.29 Å / Num. obs: 27118 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 58.07 Å2 / CC1/2: 1 / Net I/σ(I): 8.6
Reflection shellResolution: 2.07→2.11 Å / Num. unique obs: 1385 / CC1/2: 0.3

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Processing

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

5mau


Resolution: 2.09→44.4 Å / SU ML: 0.408 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 42.24
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2704 1679 7.5 %
Rwork0.2218 20720 -
obs0.2253 22399 82.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.72 Å2
Refinement stepCycle: LAST / Resolution: 2.09→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 158 32 3170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463216
X-RAY DIFFRACTIONf_angle_d0.84654366
X-RAY DIFFRACTIONf_chiral_restr0.0434440
X-RAY DIFFRACTIONf_plane_restr0.0142546
X-RAY DIFFRACTIONf_dihedral_angle_d15.8788456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.5821100.533799X-RAY DIFFRACTION4.85
2.15-2.220.4268790.4557819X-RAY DIFFRACTION39.89
2.22-2.30.47881280.46041530X-RAY DIFFRACTION73.53
2.3-2.390.41451520.39711915X-RAY DIFFRACTION92.61
2.39-2.50.40741610.352029X-RAY DIFFRACTION96.69
2.5-2.630.38021650.31192043X-RAY DIFFRACTION97.18
2.63-2.790.34121650.28721999X-RAY DIFFRACTION97.79
2.79-3.010.36631620.26722082X-RAY DIFFRACTION98.08
3.01-3.310.29921650.24372038X-RAY DIFFRACTION98.22
3.31-3.790.24081620.19382048X-RAY DIFFRACTION98.31
3.79-4.780.21881660.16752049X-RAY DIFFRACTION98.75
4.78-44.40.21141640.18382069X-RAY DIFFRACTION98.85
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)
13.910529890280.8391686604372.185039361112.72618995092.450214501797.29354523764-0.0331183535574-0.00647163138890.00796360420514-0.00584708623825-0.1000015194340.192981863141-0.0751035074656-0.5046895332790.1722145519520.378733876801-0.1013821186620.01428647672440.3510348798220.007834799405950.259784046327-24.5777828216-9.473850283176.38534973234
22.461227082840.5220112533871.482252010861.849640510610.7294043334085.27417060501-0.09380906266960.527253296861-0.0328776450321-0.2723648512420.206719243096-0.242004460541-0.09017562183520.800671782928-0.1090410796610.335780351253-0.08372401700310.03625807884450.407113726104-0.06375175265580.288436611935-9.32769858445-10.2002824967.81787643198
35.67212534006-1.49929509952-4.007563269893.22893696645-1.302270025895.484699173260.11238565634-0.2133611629610.2186746218970.044415469946-0.301376602720.778376487015-0.409662308548-0.8764005484550.1896953538380.491025004999-0.0895564838894-0.009811514048960.688312180632-0.1518394392150.496142958388-30.41006199143.338967639136.8795243968
42.778690648240.2254503580770.253743572721.950956554461.22733875623.40307766598-0.02905844442480.05402167100090.01653426689030.1438854724040.00635524627940.0464928117070.0362709660102-0.1802953084850.03995115537420.601610526623-0.200205771532-0.03575735135040.486580412036-0.06080573993770.34042258306-11.8137423186-1.5652648148932.4791107797
52.68806897615-0.04143037763620.5741123269971.372963888841.3263379973.91221711504-0.0409973526669-0.2640170146590.2321280516940.03105507362070.01238239623240.0521338026231-0.3127774918860.3017108695860.01924173075470.570740460523-0.133394325855-0.02729095748090.397652870155-0.0477668083580.400089318991-13.10898135323.5756444947238.3841876519
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 63 )AA2 - 631 - 62
22chain 'A' and (resid 64 through 182 )AA64 - 18263 - 181
33chain 'B' and (resid 2 through 49 )BF2 - 491 - 48
44chain 'B' and (resid 50 through 108 )BF50 - 10849 - 107
55chain 'B' and (resid 109 through 182 )BF109 - 182108 - 181

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