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- PDB-5a13: Crystal structure of Chlorite Dismutase from Magnetospirillum sp.... -

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Basic information

Entry
Database: PDB / ID: 5a13
TitleCrystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with thiocyanate
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
PROTOPORPHYRIN IX CONTAINING FE / THIOCYANATE ION / Chlorite dismutase
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM SP. (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.2Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.3Jan 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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 / _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. THE SHEETS PRESENTED AS "FA" 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 "GA" 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 "HA" 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 "IA" 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 "JA" 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
F: CHLORITE DISMUTASE
G: CHLORITE DISMUTASE
H: CHLORITE DISMUTASE
I: CHLORITE DISMUTASE
J: CHLORITE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,09644
Polymers271,06110
Non-polymers8,03534
Water37,5252083
1
F: CHLORITE DISMUTASE
G: CHLORITE DISMUTASE
H: CHLORITE DISMUTASE
I: CHLORITE DISMUTASE
J: CHLORITE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,54822
Polymers135,5305
Non-polymers4,01817
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23230 Å2
ΔGint-187.1 kcal/mol
Surface area43170 Å2
MethodPISA
2
A: CHLORITE DISMUTASE
B: CHLORITE DISMUTASE
C: CHLORITE DISMUTASE
D: CHLORITE DISMUTASE
E: CHLORITE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,54822
Polymers135,5305
Non-polymers4,01817
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23060 Å2
ΔGint-186.3 kcal/mol
Surface area43040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.026, 124.482, 133.376
Angle α, β, γ (deg.)90.00, 92.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CHLORITE DISMUTASE


Mass: 27106.053 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) MAGNETOSPIRILLUM SP. (magnetotactic) / References: UniProt: A0A0M3KL47*PLUS, chlorite O2-lyase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2083 / 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: 2.62 Å3/Da / Density % sol: 53.1 % / Description: NONE
Crystal growpH: 8.5 / Details: 20% PEG 4000, 0.1 M TRIS-HCL PH 8.5, 0.2 M LI2SO4

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jan 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.75→49.11 Å / Num. obs: 261153 / % possible obs: 99.7 % / Observed criterion σ(I): 2.2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q08

3q08


Resolution: 1.75→49.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.16 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18349 12628 4.8 %RANDOM
Rwork0.15129 ---
obs0.15287 248487 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.06 Å2
2--0.69 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18900 0 544 2083 21527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01920326
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219609
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.98927802
X-RAY DIFFRACTIONr_angle_other_deg0.882345019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35752545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50823.846832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.039153445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1315121
X-RAY DIFFRACTIONr_chiral_restr0.120.23167
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222871
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024650
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_it3.9711.6489837
X-RAY DIFFRACTIONr_mcbond_other3.9711.6479826
X-RAY DIFFRACTIONr_mcangle_it4.3252.44512300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.1141.91210489
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 926 -
Rwork0.232 18285 -
obs--99.75 %

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