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- PDB-7asb: Crystal structure of dimeric chlorite dismutase variant Q74E (CCl... -

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Basic information

Entry
Database: PDB / ID: 7asb
TitleCrystal structure of dimeric chlorite dismutase variant Q74E (CCld Q74E) from Cyanothece sp. PCC7425
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / chlorite dismutase / heme enzyme
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / 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 / hydrogen peroxide-dependent heme synthase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchmidt, D. / Mlynek, G. / Djinovic-Carugo, K. / Obinger, C.
CitationJournal: Biochemistry / Year: 2021
Title: Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis.
Authors: Schmidt, D. / Serra, I. / Mlynek, G. / Pfanzagl, V. / Hofbauer, S. / Furtmuller, P.G. / Djinovic-Carugo, K. / Van Doorslaer, S. / Obinger, C.
History
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 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

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Assembly

Deposited unit
A: Chlorite dismutase
B: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,16516
Polymers43,6642
Non-polymers2,50114
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, HPLC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-62 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.160, 52.738, 54.772
Angle α, β, γ (deg.)107.410, 99.143, 108.984
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: 21831.865 Da / Num. of mol.: 2 / Mutation: Q74E
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 , 6 types, 286 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES 6.5 pH, 0.15 M MgSO4, 28 % w/v PEG 3350, 3 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 1.4→30.98 Å / Num. obs: 90357 / % possible obs: 92.53 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.09 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06724 / Rpim(I) all: 0.04186 / Rrim(I) all: 0.07945 / Net I/σ(I): 10.09
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.195 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 8896 / CC1/2: 0.571 / CC star: 0.852 / Rpim(I) all: 0.7172 / % possible all: 91.39

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Processing

Software
NameVersionClassification
PHENIXdev_3885refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MAU

5mau


Resolution: 1.4→30.98 Å / SU ML: 0.1794 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.2571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.193 1384 1.53 %
Rwork0.1619 88917 -
obs0.1624 90301 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.79 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 167 272 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01763305
X-RAY DIFFRACTIONf_angle_d1.89024491
X-RAY DIFFRACTIONf_chiral_restr0.1136448
X-RAY DIFFRACTIONf_plane_restr0.0128570
X-RAY DIFFRACTIONf_dihedral_angle_d20.665471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.33721510.31688737X-RAY DIFFRACTION91.4
1.45-1.510.28441210.2648819X-RAY DIFFRACTION90.81
1.51-1.580.28431360.22668567X-RAY DIFFRACTION89.69
1.58-1.660.2121440.18769018X-RAY DIFFRACTION93.51
1.66-1.760.23941270.16799056X-RAY DIFFRACTION93.87
1.76-1.90.17751440.14768902X-RAY DIFFRACTION93.22
1.9-2.090.17811310.14318759X-RAY DIFFRACTION91.18
2.09-2.390.1871490.14348948X-RAY DIFFRACTION93.22
2.39-3.020.16971370.1589166X-RAY DIFFRACTION95.12
3.02-30.980.18081440.14998945X-RAY DIFFRACTION93.33

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