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

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Basic information

Entry
Database: PDB / ID: 1vzg
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
HEXACYANOFERRATE(3-) / : / Desulfoferrodoxin
Similarity search - Component
Biological speciesDESULFOVIBRIO BAARSII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 Photoreduction
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 1.3Dec 13, 2023Group: 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 / 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DESULFOFERRODOXIN
B: DESULFOFERRODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9249
Polymers28,2372
Non-polymers6877
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.130, 67.650, 82.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: Q46495, superoxide reductase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6FeN6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.07 Å3/Da / Density % sol: 36 %
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: ID14-4 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2003 / Details: MIRRORS
RadiationMonochromator: SI 111 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.69→37.49 Å / Num. obs: 26217 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellRedundancy: 2.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DFX

1dfx


Resolution: 1.69→37.49 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1920830.55 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CYSTEINES FROM THE CENTER I WERE MODELED IN ALTERNATE CONFORMATIONS, AS WELL AS CENTER I IRONS AND RESIDUES 84 TO 86
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1285 5 %RANDOM
Rwork0.205 ---
obs0.205 25836 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1442 Å2 / ksol: 0.373404 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.69→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 31 161 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 1.69→1.8 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 209 5.2 %
Rwork0.262 --
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FER.PARAMFER.TOP
X-RAY DIFFRACTION5PROTEIN-CIS.PARAM

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