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- PDB-2nyb: Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1... -

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Basic information

Entry
Database: PDB / ID: 2nyb
TitleCrystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution
ComponentsSuperoxide dismutase [FE]
KeywordsOXIDOREDUCTASE / Iron Superoxide Dismutase Q69E / FeSOD
Function / homology
Function and homology information


response to superoxide / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / oxidoreductase activity / iron ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / OXYGEN ATOM / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsPorta, J.C. / Vahedi-Faridi, A. / Borgstahl, G.E.O.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: How Can a Single Second Sphere Amino Acid Substitution Cause Reduction Midpoint Potential Changes of Hundreds of Millivolts?
Authors: Yikilmaz, E. / Porta, J. / Grove, L.E. / Vahedi-Faridi, A. / Bronshteyn, Y. / Brunold, T.C. / Borgstahl, G.E. / Miller, A.F.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [FE]
B: Superoxide dismutase [FE]
C: Superoxide dismutase [FE]
D: Superoxide dismutase [FE]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,90912
Polymers84,6224
Non-polymers2878
Water20,6091144
1
A: Superoxide dismutase [FE]
B: Superoxide dismutase [FE]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4556
Polymers42,3112
Non-polymers1444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-9 kcal/mol
Surface area16440 Å2
MethodPISA
2
C: Superoxide dismutase [FE]
D: Superoxide dismutase [FE]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4556
Polymers42,3112
Non-polymers1444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-8 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.508, 107.596, 84.120
Angle α, β, γ (deg.)90.000, 94.890, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homotetramer generated by the two-fold axis: -x, y+1/2, -z.

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Components

#1: Protein
Superoxide dismutase [FE] / Iron Superoxide dismutase


Mass: 21155.471 Da / Num. of mol.: 4 / Mutation: Q69E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sodB, b1656, JW1648 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGD3, superoxide dismutase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1144 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 100 mM Ammonium acetate pH 5.7, 10 mM Sodium citrate, 22.5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.88557 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.1→30.29 Å / Num. all: 283939 / Num. obs: 283939 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 1.05 % / Biso Wilson estimate: 13.753 Å2 / Limit h max: 33 / Limit h min: -39 / Limit k max: 97 / Limit k min: 0 / Limit l max: 76 / Limit l min: 0 / Rsym value: 0.027 / Net I/σ(I): 28

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→30.29 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.902 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 14104 5 %RANDOM
Rwork0.16 ---
all0.16 269833 --
obs0.16 269833 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.13 Å2
2--0.04 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.1→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6661 0 8 1144 7813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0236937
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.9229540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1765911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90124.859319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.187151034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2581514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025606
X-RAY DIFFRACTIONr_nbd_refined0.1950.23624
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.2852
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.270
X-RAY DIFFRACTIONr_mcbond_it0.5481.54376
X-RAY DIFFRACTIONr_mcangle_it0.86826942
X-RAY DIFFRACTIONr_scbond_it1.28733002
X-RAY DIFFRACTIONr_scangle_it1.7074.52598
X-RAY DIFFRACTIONr_rigid_bond_restr0.85437378
X-RAY DIFFRACTIONr_sphericity_free2.11431148
X-RAY DIFFRACTIONr_sphericity_bonded1.90736661
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 961 -
Rwork0.213 17777 -
obs-18738 100 %

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