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- PDB-1vzi: Structure of superoxide reductase bound to ferrocyanide and activ... -

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Basic information

Entry
Database: PDB / ID: 1vzi
TitleStructure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction
ComponentsDESULFOFERRODOXIN
KeywordsOXIDOREDUCTASE / FERROCYANIDE / MICROSPECTROPHOTOMETRY / REDOX STATES / PHOTOREDUCTION / DINUCLEAR IRON CLUSTER / ELECTRON TRANSPORT
Function / homology
Function and homology information


superoxide reductase / superoxide reductase activity / removal of superoxide radicals / iron ion binding
Similarity search - Function
Desulphoferrodoxin, N-terminal domain / Desulfoferrodoxin / Desulfoferrodoxin, N-terminal domain / Desulfoferrodoxin, N-terminal domain superfamily / Desulfoferrodoxin, N-terminal domain / SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Rubrerythrin, domain 2 ...Desulphoferrodoxin, N-terminal domain / Desulfoferrodoxin / Desulfoferrodoxin, N-terminal domain / Desulfoferrodoxin, N-terminal domain superfamily / Desulfoferrodoxin, N-terminal domain / SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Rubrerythrin, domain 2 / Single Sheet / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Desulfoferrodoxin
Similarity search - Component
Biological speciesDESULFOVIBRIO BAARSII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsAdam, V. / Royant, A. / Niviere, V. / Molina-Heredia, F.P. / Bourgeois, D.
CitationJournal: Structure / Year: 2004
Title: Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction.
Authors: Adam, V. / Royant, A. / Niviere, V. / Molina-Heredia, F.P. / Bourgeois, D.
History
DepositionMay 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DESULFOFERRODOXIN
B: DESULFOFERRODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,68212
Polymers28,2372
Non-polymers44510
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.608, 123.608, 73.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

21A-2109-

HOH

31A-2219-

HOH

41B-2121-

HOH

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Components

#1: Protein DESULFOFERRODOXIN / SUPEROXIDE REDUCTASE / DFX / SOR


Mass: 14118.362 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO BAARSII (bacteria) / Plasmid: PMLE47A / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q46495, superoxide reductase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNON-HEME IRON PROTEIN. CATALYSES SUPEROXIDE ANION + 2 H(+) = H(2)O(2). COFACTOR: BINDS 1 ...NON-HEME IRON PROTEIN. CATALYSES SUPEROXIDE ANION + 2 H(+) = H(2)O(2). COFACTOR: BINDS 1 DESULFOFERRODOXIN-LIKE FES(4) SITE AND 1 ENGINEERED MUTATION GLU 47 TO ALA, CHAINS A AND B

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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: 2.47 Å3/Da / Density % sol: 38 %
Crystal growpH: 8 / Details: 18% PEG 4000, 100 MM TRIS PH 8.0, 100 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.923
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 23, 2003 / Details: MIRRORS
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.923 Å / Relative weight: 1
ReflectionResolution: 1.15→45 Å / Num. obs: 93621 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.6
Reflection shellRmerge(I) obs: 0.41 / % possible all: 98.1

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→45 Å / Num. parameters: 22352 / Num. restraintsaints: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF). CHLORIDE ION IN ACTIVE SITE II (MONOMER B) IS MODELED IN DUAL CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
all0.1427 98585 --
obs--99.1 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2480.25
Refinement stepCycle: LAST / Resolution: 1.15→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 10 518 2484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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