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- PDB-5k90: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -

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Basic information

Entry
Database: PDB / ID: 5k90
TitleCrystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 in complex with isothiocyanate
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / chlorite dismutase / cyanobacteria / heme / ferredoxin-like fold
Function / homology
Function and homology information


oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #3420 / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / isothiocyanate / Chlorite dismutase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsPuehringer, D. / Schaffner, I. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
CitationJournal: ACS Catal / Year: 2017
Title: Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies.
Authors: Schaffner, I. / Mlynek, G. / Flego, N. / Puhringer, D. / Libiseller-Egger, J. / Coates, L. / Hofbauer, S. / Bellei, M. / Furtmuller, P.G. / Battistuzzi, G. / Smulevich, G. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 2, 2019Group: Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list

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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
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,07124
Polymers87,3244
Non-polymers3,74820
Water14,430801
1
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,47711
Polymers43,6622
Non-polymers1,8169
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59413
Polymers43,6622
Non-polymers1,93211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.759, 54.631, 94.096
Angle α, β, γ (deg.)99.800, 94.820, 99.170
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Chlorite dismutase /


Mass: 21830.881 Da / Num. of mol.: 4
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 / Details (production host): pET-52b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B8HNS6

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Non-polymers , 6 types, 821 molecules

#2: Chemical
ChemComp-IS8 / isothiocyanate / Isothiocyanate


Mass: 59.090 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHNS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 801 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15 M MgSO4, 0.1 M MES pH 6.5, 25% (w/v) PEG3350, 10 mM NaSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2015
Details: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.28→46.775 Å / Num. obs: 242310 / % possible obs: 93 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07663 / Net I/σ(I): 4.99
Reflection shellResolution: 1.28→1.326 Å / Redundancy: 1.8 % / Rmerge(I) obs: 2.588 / Mean I/σ(I) obs: 0.27 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIXdev_2712refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→46.775 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 37.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 11850 4.94 %
Rwork0.21 228063 -
obs0.2113 239913 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.79 Å2 / Biso mean: 28.0031 Å2 / Biso min: 12.01 Å2
Refinement stepCycle: final / Resolution: 1.28→46.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 430 801 7010
Biso mean--27.65 32.34 -
Num. residues----698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156214
X-RAY DIFFRACTIONf_angle_d1.3758441
X-RAY DIFFRACTIONf_chiral_restr0.096847
X-RAY DIFFRACTIONf_plane_restr0.011067
X-RAY DIFFRACTIONf_dihedral_angle_d15.7742266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2799-1.29440.50793820.48897451783391
1.2944-1.30960.48113600.47367315767590
1.3096-1.32560.4854070.47137640804793
1.3256-1.34240.51913810.46277436781792
1.3424-1.36010.47684050.44197599800493
1.3601-1.37870.42934230.43227512793593
1.3787-1.39840.43313940.42337765815994
1.3984-1.41930.43444050.41117475788093
1.4193-1.44140.42913910.39337579797092
1.4414-1.46510.40193790.37187518789793
1.4651-1.49030.36774070.34537509791692
1.4903-1.51740.3254020.31977657805993
1.5174-1.54660.31394090.30117414782392
1.5466-1.57820.35533880.29467591797993
1.5782-1.61250.30953850.27437525791092
1.6125-1.650.28183830.25977561794493
1.65-1.69130.30293780.25317492787092
1.6913-1.7370.2723850.24577529791493
1.737-1.78810.27493950.24577460785592
1.7881-1.84590.25323950.22327488788392
1.8459-1.91180.25124100.20587467787792
1.9118-1.98840.22184120.18427658807094
1.9884-2.07890.20854100.17447799820996
2.0789-2.18850.21353860.17057896828296
2.1885-2.32560.18984000.15947789818996
2.3256-2.50510.18864100.15627830824096
2.5051-2.75720.17844240.15737745816995
2.7572-3.15610.19913740.16347868824297
3.1561-3.97610.15984200.14817773819395
3.9761-46.80670.16053500.15967722807295

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