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

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Basic information

Entry
Database: PDB / ID: 5mau
TitleCrystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 (pH 6.5)
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 / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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
DepositionNov 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 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 17, 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2678
Polymers43,6622
Non-polymers1,6056
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-46 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.120, 52.650, 54.730
Angle α, β, γ (deg.)107.22, 99.22, 108.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Chlorite dismutase


Mass: 21830.881 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 59.31 %
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) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2016
Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing
RadiationMonochromator: Standard ESRF channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→46.381 Å / Num. obs: 115659 / % possible obs: 95 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08048 / Net I/σ(I): 10.55
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 7 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.99 / CC1/2: 0.399 / % possible all: 91.81

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXDEV_2712refinement
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QPI

3qpi


Resolution: 1.3→46.38 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.176 1987 1.72 %
Rwork0.147 --
obs0.148 115590 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.05 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 109 498 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173151
X-RAY DIFFRACTIONf_angle_d1.4814296
X-RAY DIFFRACTIONf_dihedral_angle_d19.2831161
X-RAY DIFFRACTIONf_chiral_restr0.103428
X-RAY DIFFRACTIONf_plane_restr0.011551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33250.36641290.34687821X-RAY DIFFRACTION92
1.3325-1.36860.32231470.3077875X-RAY DIFFRACTION92
1.3686-1.40880.33591320.27357996X-RAY DIFFRACTION93
1.4088-1.45430.26031400.24347943X-RAY DIFFRACTION93
1.4543-1.50630.29611380.21927998X-RAY DIFFRACTION94
1.5063-1.56660.21781460.17847997X-RAY DIFFRACTION94
1.5666-1.63790.21021360.15268117X-RAY DIFFRACTION95
1.6379-1.72430.18051520.13388116X-RAY DIFFRACTION95
1.7243-1.83230.18931320.13048147X-RAY DIFFRACTION95
1.8323-1.97380.1761480.12378210X-RAY DIFFRACTION96
1.9738-2.17240.15851440.11518242X-RAY DIFFRACTION97
2.1724-2.48670.1431500.11798308X-RAY DIFFRACTION97
2.4867-3.13290.15041450.14028378X-RAY DIFFRACTION98
3.1329-46.41050.16351480.14418455X-RAY DIFFRACTION99

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