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- PDB-1za5: Q69H-FeSOD -

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Basic information

Entry
Database: PDB / ID: 1za5
TitleQ69H-FeSOD
ComponentsSuperoxide dismutase [Fe]
KeywordsOXIDOREDUCTASE / H-bonding redox tuning superoxide dismutase proton-coupled electron transfer
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 / cytoplasm / cytosol
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
: / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYikilmaz, E. / Rodgers, D.W. / Miller, A.F.
CitationJournal: Biochemistry / Year: 2006
Title: The Crucial Importance of Chemistry in the Structure-Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase.
Authors: Yikilmaz, E. / Rodgers, D.W. / Miller, A.F.
History
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9298
Polymers42,3292
Non-polymers6006
Water8,269459
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.202, 84.921, 61.634
Angle α, β, γ (deg.)90.00, 108.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Superoxide dismutase [Fe]


Mass: 21164.504 Da / Num. of mol.: 2 / Mutation: Q69H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sodB / Production host: Escherichia coli (E. coli) / Strain (production host): QC774 / References: UniProt: P0AGD3, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Fragment: Fe / Mutation: NA, metal ion / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.66
Details: MgCl2, PEG8000, pH 8.66, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 35545 / Num. obs: 32845 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.4 Å2
Reflection shellResolution: 1.8→1.88 Å / % possible all: 43

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 973646.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3289 10 %RANDOM
Rwork0.199 ---
all0.202 32845 --
obs0.199 32845 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7353 Å2 / ksol: 0.357978 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-8.31 Å20 Å28.96 Å2
2---7.4 Å20 Å2
3----0.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 34 459 3501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 302 10 %
Rwork0.344 2732 -
obs--49.1 %
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 DIFFRACTION4trs.partrs.top

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