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- PDB-1dfx: DESULFOFERRODOXIN FROM DESULFOVIBRIO DESULFURICANS, ATCC 27774 -

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Basic information

Entry
Database: PDB / ID: 1dfx
TitleDESULFOFERRODOXIN FROM DESULFOVIBRIO DESULFURICANS, ATCC 27774
ComponentsDESULFOFERRODOXIN
KeywordsELECTRON TRANSPORT / NON-HEME IRON PROTEIN
Function / homology
Function and homology information


superoxide reductase / superoxide reductase activity / removal of superoxide radicals / iron ion binding
Similarity search - Function
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 / Immunoglobulin-like ...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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Desulfoferrodoxin
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTIPLE WAVELENGTH ANOMALOUS DISPERSION (MAD) / Resolution: 1.9 Å
AuthorsCoelho, A.V. / Matias, P.M. / Carrondo, M.A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 1997
Title: Desulfoferrodoxin Structure Determined by MAD Phasing and Refinement to 1.9 Angstroms Resolution Reveals a Unique Combination of a Tetrahedral Fes4 Centre with a Square Pyramidal Fesn4 Centre
Authors: Coelho, A.V. / Matias, P. / Fulop, V. / Thompson, A. / Gonzalez, A. / Carrondo, M.A.
#1: Journal: Protein Sci. / Year: 1996
Title: Preliminary Crystallographic Analysis of the Oxidized Form of a Two Mono-Nuclear Iron Centres Protein from Desulfovibrio Desulfuricans Atcc 27774
Authors: Coelho, A.V. / Matias, P.M. / Carrondo, M.A. / Tavares, P. / Moura, J.J. / Moura, I. / Fulop, V. / Hajdu, J. / Le Gall, J.
History
DepositionSep 3, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DESULFOFERRODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0564
Polymers13,9041
Non-polymers1523
Water1,27971
1
A: DESULFOFERRODOXIN
hetero molecules

A: DESULFOFERRODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1118
Polymers27,8082
Non-polymers3046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3440 Å2
ΔGint-68 kcal/mol
Surface area11430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.500, 112.500, 63.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-150-

CA

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Components

#1: Protein DESULFOFERRODOXIN


Mass: 13903.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / References: UniProt: P22076
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.8 Å3/Da / Density % sol: 55 % / Description: MAD DATA COLLECTED AT ESRF BM-14
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 0.1 M HEPES, CACL2 0.2 M, PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Coelho, A.V., (1996) Protein Sci., 5, 1189.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(w/v)PEG40001reservoir
20.1 MHEPES1reservoir
30.2 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.994
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1992 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.994 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 11867 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.26 / % possible all: 96.3
Reflection
*PLUS
Num. measured all: 25678
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameClassification
SHELXL-93model building
SHELXL-93refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93phasing
RefinementMethod to determine structure: MULTIPLE WAVELENGTH ANOMALOUS DISPERSION (MAD)
Resolution: 1.9→20 Å / Num. parameters: 4254 / Num. restraintsaints: 3852 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE REFINEMENT WAS STARTED WITH X-PLOR. NO GEOMETRICAL RESTRAINTS WERE IMPOSED BETWEEN THE IRON ATOMS AND THEIR LIGANDS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 689 5 %RANDOM
all0.2 13564 --
obs0.2 -97.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeOccupancy sum non hydrogen: 1027
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 3 71 1048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.274
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.141
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg30.7

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