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- PDB-5k91: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -

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Basic information

Entry
Database: PDB / ID: 5k91
TitleCrystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 in complex with fluoride
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / chlorite dismutase / cyanobacteria / heme / ferredoxin-like fold
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / 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
FLUORIDE ION / PROTOPORPHYRIN IX CONTAINING FE / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)90,42618
Polymers87,3244
Non-polymers3,10214
Water17,673981
1
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2139
Polymers43,6622
Non-polymers1,5517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2139
Polymers43,6622
Non-polymers1,5517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.146, 54.697, 94.266
Angle α, β, γ (deg.)99.060, 94.840, 99.040
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. PCC 7425 (bacteria) / 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 , 5 types, 995 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Chemical
ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: F
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 981 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.15 M MgSO4, 0.1 M MES pH 6.5, 22% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2016
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.18→46.345 Å / Num. obs: 294532 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06142 / Net I/σ(I): 6.71
Reflection shellResolution: 1.18→1.222 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 0.98 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIXdev_2712refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QPI

3qpi


Resolution: 1.18→46.345 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 36.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 14736 5.01 %
Rwork0.1901 279382 -
obs0.1917 294118 90.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.41 Å2 / Biso mean: 22.4235 Å2 / Biso min: 7.85 Å2
Refinement stepCycle: final / Resolution: 1.18→46.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 356 981 7121
Biso mean--19.38 34.12 -
Num. residues----699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0236286
X-RAY DIFFRACTIONf_angle_d2.1118571
X-RAY DIFFRACTIONf_chiral_restr0.12861
X-RAY DIFFRACTIONf_plane_restr0.0141096
X-RAY DIFFRACTIONf_dihedral_angle_d14.9922303
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 (%)
1.1799-1.19330.44014580.41418900935886
1.1933-1.20730.39294530.38149041949487
1.2073-1.22210.3654900.35849001949187
1.2221-1.23750.35524870.33738913940087
1.2375-1.25380.35854370.33339103954088
1.2538-1.2710.35634680.32869260972889
1.271-1.28910.33544580.31429220967889
1.2891-1.30840.32384810.30359202968389
1.3084-1.32880.30064630.29029245970889
1.3288-1.35060.29864560.26449201965789
1.3506-1.37390.27954980.25959117961588
1.3739-1.39890.26014840.24868851933586
1.3989-1.42580.25915060.22678844935086
1.4258-1.45490.22165340.199294661000092
1.4549-1.48650.22534940.19569502999692
1.4865-1.52110.21685000.185795771007792
1.5211-1.55920.22944890.1829505999492
1.5592-1.60130.20784850.16795511003692
1.6013-1.64850.1825100.16289484999492
1.6485-1.70170.17564950.15729472996792
1.7017-1.76250.18395450.15419428997391
1.7625-1.83310.20234700.16219233970390
1.8331-1.91650.20694650.16698684914984
1.9165-2.01750.19575560.165897781033495
2.0175-2.14390.18014780.161198311030995
2.1439-2.30950.19255140.16497831029795
2.3095-2.54180.22844890.166597461023594
2.5418-2.90960.23255390.1795361007593
2.9096-3.66560.19874650.18088938940386
3.6656-46.38040.21025690.183399701053997

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