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- PDB-4bfj: Superoxide reductase (Neelaredoxin) from Archaeoglobus fulgidus E... -

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Basic information

Entry
Database: PDB / ID: 4bfj
TitleSuperoxide reductase (Neelaredoxin) from Archaeoglobus fulgidus E12V mutant
ComponentsSUPEROXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / OXYGEN DETOXIFICATION
Function / homology
Function and homology information


superoxide reductase / superoxide reductase activity / iron ion binding
Similarity search - Function
SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Putative superoxide reductase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBandeiras, T.M. / Rodrigues, J.V. / Sousa, C.M. / Barradas, A.R. / Pinho, F.G. / Pinto, A.F. / Teixeira, M. / Matias, P.M. / Romao, C.V.
CitationJournal: To be Published
Title: Understanding the Role of Key Residues in the Superoxide Reductase Molecular Mechanism, Exploring Archaeoglobus Fulgidus Sor Structure
Authors: Bandeiras, T.M. / Rodrigues, J.V. / Sousa, C.M. / Barradas, A.R. / Pinho, F.G. / Pinto, A.F. / Teixeira, M. / Matias, P.M. / Romao, C.V.
History
DepositionMar 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE REDUCTASE
B: SUPEROXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4774
Polymers27,3652
Non-polymers1122
Water0
1
A: SUPEROXIDE REDUCTASE
B: SUPEROXIDE REDUCTASE
hetero molecules

A: SUPEROXIDE REDUCTASE
B: SUPEROXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9548
Polymers54,7304
Non-polymers2234
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area8640 Å2
ΔGint-51.5 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.790, 98.970, 105.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein SUPEROXIDE REDUCTASE / / SOR


Mass: 13682.566 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PT7-7/NAFE12VA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: O29903
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe

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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: 4.4 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M HEPES PH 7.0 AND 26% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9786
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→40.7 Å / Num. obs: 12125 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.17 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.87
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.08 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.19 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSPROGRAM PACKAGEdata reduction
XDSPROGRAM PACKAGEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGL

4bgl


Resolution: 2.8→41.542 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 1067 4.8 %
Rwork0.1775 --
obs0.18 12102 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→41.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 2 0 1920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121984
X-RAY DIFFRACTIONf_angle_d1.2612708
X-RAY DIFFRACTIONf_dihedral_angle_d14.385688
X-RAY DIFFRACTIONf_chiral_restr0.067296
X-RAY DIFFRACTIONf_plane_restr0.005344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.92740.3671550.28842638X-RAY DIFFRACTION97
2.9274-3.08170.32671300.252707X-RAY DIFFRACTION98
3.0817-3.27470.27491420.21512663X-RAY DIFFRACTION98
3.2747-3.52740.23081240.17952640X-RAY DIFFRACTION97
3.5274-3.88220.23331350.16842692X-RAY DIFFRACTION97
3.8822-4.44340.17811450.1422624X-RAY DIFFRACTION97
4.4434-5.59610.20751210.15782657X-RAY DIFFRACTION96
5.5961-41.54650.25291150.1892634X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.23621.6917-5.14425.4469-4.59227.6636-0.5538-0.3687-0.2548-0.7811-0.064-0.09551.00140.75310.73641.07680.0374-0.09590.753-0.13970.582216.8522-2.88344.0599
25.4849-0.2617-0.00642.6604-0.87525.54090.14480.5654-0.5042-0.5309-0.10830.19960.36970.4758-0.05830.75430.102-0.02720.6132-0.12340.548714.8765-2.462914.9132
33.95933.6029-0.28345.1138-3.18174.5721-0.3609-0.07550.2704-0.56330.59470.44991.2467-0.1684-0.1780.9654-0.0371-0.12040.5271-0.10460.71185.8762-22.654227.9491
42.8135-0.3081-0.22043.0808-0.66794.53090.13120.1588-0.6173-0.1753-0.1010.46580.80290.06370.01450.6835-0.0376-0.02930.4522-0.10070.64248.0589-11.608226.5548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 33 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 34 THROUGH 125 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 2 THROUGH 34 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 35 THROUGH 125 )

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