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- PDB-1t6u: Nickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure -

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Basic information

Entry
Database: PDB / ID: 1t6u
TitleNickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure
ComponentsSuperoxide dismutase [Ni]
KeywordsOXIDOREDUCTASE / Nickel / 4-helix bundle / hexamer / superoxide dismutase / NiSOD / SOD / high resolution
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
NICKEL (II) ION / Superoxide dismutase [Ni]
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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]
D: Superoxide dismutase [Ni]
E: Superoxide dismutase [Ni]
F: Superoxide dismutase [Ni]
G: Superoxide dismutase [Ni]
H: Superoxide dismutase [Ni]
I: Superoxide dismutase [Ni]
J: Superoxide dismutase [Ni]
K: Superoxide dismutase [Ni]
L: Superoxide dismutase [Ni]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,59624
Polymers158,89212
Non-polymers70412
Water34,6971926
1
A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]
D: Superoxide dismutase [Ni]
E: Superoxide dismutase [Ni]
F: Superoxide dismutase [Ni]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,79812
Polymers79,4466
Non-polymers3526
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-91 kcal/mol
Surface area26850 Å2
MethodPISA
2
G: Superoxide dismutase [Ni]
H: Superoxide dismutase [Ni]
I: Superoxide dismutase [Ni]
J: Superoxide dismutase [Ni]
K: Superoxide dismutase [Ni]
L: Superoxide dismutase [Ni]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,79812
Polymers79,4466
Non-polymers3526
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-82 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.147, 111.680, 106.834
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is hexameric

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Components

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


Mass: 13241.003 Da / Num. of mol.: 12 / 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: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1926 / 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: 2.08 Å3/Da / Density % sol: 48 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. all: 347604 / Num. obs: 347567 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.055 / Net I/σ(I): 18.5
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 29263 / Rsym value: 0.365 / % possible all: 79.8

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T6I

1t6i


Resolution: 1.3→50 Å / Num. parameters: 119964 / Num. restraintsaints: 143755 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 15723 4.7 %RANDOM
Rwork0.1579 ---
all-347567 --
obs-347567 90.3 %-
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 10899 / Occupancy sum non hydrogen: 13110
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11254 0 12 1926 13192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0206
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.084
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
1.3-1.360.29X-RAY DIFFRACTION34219
1.36-1.420.257X-RAY DIFFRACTION33434
1.42-1.480.22X-RAY DIFFRACTION32014
1.48-1.570.183X-RAY DIFFRACTION33679
1.57-1.670.162X-RAY DIFFRACTION32408
1.67-1.80.138X-RAY DIFFRACTION33496

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