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- PDB-1t6i: Nickel Superoxide Dismutase (NiSOD) Apo Structure -

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Basic information

Entry
Database: PDB / ID: 1t6i
TitleNickel Superoxide Dismutase (NiSOD) Apo Structure
ComponentsSuperoxide dismutase [Ni]
KeywordsOXIDOREDUCTASE / Nickel / 4-helix bundle / hexamer / superoxide dismutase / NiSOD / SOD / apo
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 / MAD / Resolution: 2.81 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 6, 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 / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)40,5393
Polymers40,5393
Non-polymers00
Water39622
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)81,0776
Polymers81,0776
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10490 Å2
ΔGint-52 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.430, 110.241, 110.659
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 generated 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: 13512.885 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: PET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P80735, superoxide dismutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 2000, 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: ESRF / Beamline: BM14 / Wavelength: 0.911656, 0.97912, 0.979311
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 11, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9116561
20.979121
30.9793111
ReflectionResolution: 2.8→20 Å / Num. all: 9300 / Num. obs: 9300 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 63 Å2 / Rsym value: 0.059 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 4.3 / Num. unique all: 912 / Rsym value: 0.267 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.81→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 309608.65 / Data cutoff high rms absF: 309608.65 / 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
Rfree0.292 927 10.4 %RANDOM
Rwork0.235 ---
obs0.238 8940 95.9 %-
all-9288 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.289707 e/Å3
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1--22.36 Å20 Å20 Å2
2---5.57 Å20 Å2
3---27.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 0 22 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.13
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 2.81→2.98 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 113 8.8 %
Rwork0.347 1177 -
obs--84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWAT.TOP

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