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- PDB-5k8z: Crystal structure of dimeric chlorite dismutase from Cyanothece s... -

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Basic information

Entry
Database: PDB / ID: 5k8z
TitleCrystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 (pH 8.5)
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
PROTOPORPHYRIN IX CONTAINING FE / HYDROXIDE ION / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPuehringer, D. / Schaffner, I. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins, BioToP) Austria
Austrian Science FundFWF P25270 Austria
Austrian Science FundFWF P22276 Austria
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)90,33016
Polymers87,3244
Non-polymers3,00712
Water14,232790
1
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1658
Polymers43,6622
Non-polymers1,5036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chlorite dismutase
D: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1658
Polymers43,6622
Non-polymers1,5036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.858, 72.833, 112.494
Angle α, β, γ (deg.)90.000, 94.570, 90.000
Int Tables number4
Space group name H-MP1211

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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)
Gene: Cyan7425_1434 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B8HNS6

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Non-polymers , 5 types, 802 molecules

#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2015 / Details: KB-mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.55→44.428 Å / Num. obs: 127776 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1482 / Net I/σ(I): 6.24
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 0.89 / % possible all: 100

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Processing

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

3qpi


Resolution: 1.55→44.428 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1311 1.03 %
Rwork0.1981 126337 -
obs0.1984 127648 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.73 Å2 / Biso mean: 29.4213 Å2 / Biso min: 8.2 Å2
Refinement stepCycle: final / Resolution: 1.55→44.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5968 0 388 790 7146
Biso mean--22.23 30.9 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056385
X-RAY DIFFRACTIONf_angle_d0.7268713
X-RAY DIFFRACTIONf_chiral_restr0.047889
X-RAY DIFFRACTIONf_plane_restr0.0041110
X-RAY DIFFRACTIONf_dihedral_angle_d12.1363711
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5498-1.61190.36131370.34311400714144100
1.6119-1.68530.3191500.31081398914139100
1.6853-1.77410.29261470.29231394714094100
1.7741-1.88530.2991460.2551399414140100
1.8853-2.03080.25391460.21311404814194100
2.0308-2.23520.2111490.18881399814147100
2.2352-2.55860.22231440.17921405914203100
2.5586-3.22340.20591420.17511411214254100
3.2234-44.44660.18431500.1517141831433399

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