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- PDB-1t6q: Nickel Superoxide Dismutase (NiSOD) CN-treated Apo Structure -

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Basic information

Entry
Database: PDB / ID: 1t6q
TitleNickel Superoxide Dismutase (NiSOD) CN-treated Apo Structure
ComponentsSuperoxide dismutase [Ni]
KeywordsOXIDOREDUCTASE / Nickel / 4-helix bundle / hexamer / superoxide dismutase / NiSOD / SOD / apo / cyanide
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / nickel cation binding / cytoplasm
Similarity search - Function
Nickel-containing superoxide dismutase / Superoxide dismutase, Nickel-type / Nickel-containing superoxide dismutase superfamily / Nickel-containing superoxide dismutase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Superoxide dismutase [Ni]
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBarondeau, D.P. / Kassmann, C.J. / Bruns, C.K. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: Biochemistry / Year: 2004
Title: Nickel superoxide dismutase structure and mechanism.
Authors: Barondeau, D.P. / Kassmann, C.J. / Bruns, C.K. / Tainer, J.A. / Getzoff, E.D.
History
DepositionMay 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]


Theoretical massNumber of molelcules
Total (without water)39,7233
Polymers39,7233
Non-polymers00
Water1,982110
1
A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]

A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]


Theoretical massNumber of molelcules
Total (without water)79,4466
Polymers79,4466
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area10760 Å2
ΔGint-58 kcal/mol
Surface area28390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.041, 112.491, 111.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexamer geneated from the trimer in the asymmetric unit by the operation -x,y,-z+1/2

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Components

#1: Protein Superoxide dismutase [Ni] / NiSOD / Nickel- containing superoxide dismutase


Mass: 13241.003 Da / Num. of mol.: 3 / Mutation: L85M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SODN, SOD1, SCO5254, 2SC7G11.16C / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P80735, superoxide dismutase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPEG 5000, Hepes, methanol, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.549784 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2004
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.549784 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. all: 23036 / Num. obs: 23036 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 24.9
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 5.1 / Num. unique all: 2007 / Rsym value: 0.324 / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T6I

1t6i


Resolution: 2.05→47.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 401373.55 / Data cutoff high rms absF: 401373.55 / 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
Rfree0.246 1053 4.8 %RANDOM
Rwork0.217 ---
obs0.217 22094 92.1 %-
all-23017 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1048 Å2 / ksol: 0.385898 e/Å3
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1--13.58 Å20 Å20 Å2
2---15.79 Å20 Å2
3---29.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.05→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 0 110 2765
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 134 4.7 %
Rwork0.306 2741 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWAT.TOP

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