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- PDB-5a12: Crystal structure of Chlorite Dismutase from Magnetospirillum sp.... -

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Basic information

Entry
Database: PDB / ID: 5a12
TitleCrystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with azide
ComponentsCHLORITE DISMUTASE
KeywordsOXIDOREDUCTASE / CHLORITE / CHLORIDE / DETOXIFICATION / HEME / IRON
Function / homology
Function and homology information


chlorite O2-lyase / chlorite O2-lyase activity / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Chlorite dismutase
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM SP. (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCorreia, H.D. / Santos-Silva, T.
CitationJournal: J.Phys.Chem.B / Year: 2015
Title: Ligand Binding to Chlorite Dismutase from Magnetospirillum Sp.
Authors: De Schutter, A. / Correia, H. / Freire, D.M. / Rivas, M.G. / Rizzi, A.C. / Santos-Silva, T. / Gonzalez, P.J. / Van Doorslaer, S.
History
DepositionApr 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Mar 22, 2017Group: Data collection
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
E: CHLORITE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,06323
Polymers134,0335
Non-polymers4,02918
Water31,4361745
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23480 Å2
ΔGint-173.7 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.234, 133.823, 77.622
Angle α, β, γ (deg.)90.00, 113.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CHLORITE DISMUTASE


Mass: 26806.664 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) MAGNETOSPIRILLUM SP. (magnetotactic) / References: UniProt: A0A0M3KL46*PLUS, chlorite O2-lyase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1745 / 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: 53.7 % / Description: NONE
Crystal growpH: 6 / Details: 16% PEG 6000, 0.01M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.84 Å / Num. obs: 268333 / % possible obs: 98.4 % / Observed criterion σ(I): 1.4 / Redundancy: 3.8 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 11.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.4 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q08

3q08


Resolution: 1.4→71.44 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 2.076 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15434 13525 5 %RANDOM
Rwork0.11816 ---
obs0.11994 254758 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.13 Å2
2---0.65 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→71.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9430 0 278 1745 11453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910192
X-RAY DIFFRACTIONr_bond_other_d0.0010.029831
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.99213957
X-RAY DIFFRACTIONr_angle_other_deg0.836322591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47923.981417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.515151735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2911558
X-RAY DIFFRACTIONr_chiral_restr0.1090.21591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211506
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022324
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4011.7014922
X-RAY DIFFRACTIONr_mcbond_other1.41.7014921
X-RAY DIFFRACTIONr_mcangle_it1.7242.5576166
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9441.965270
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.24920023
X-RAY DIFFRACTIONr_sphericity_free27.5035419
X-RAY DIFFRACTIONr_sphericity_bonded8.67321095
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 1016 -
Rwork0.267 18129 -
obs--94.87 %

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