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- PDB-1q0f: Crystal structure of Ni-containing superoxide dismutase with Ni-l... -

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Basic information

Entry
Database: PDB / ID: 1q0f
TitleCrystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after partial x-ray-induced reduction
ComponentsSuperoxide dismutase [Ni]
KeywordsOXIDOREDUCTASE / HOMOHEXAMER OF FOUR-HELIX BUNDLES
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 (III) ION / Superoxide dismutase [Ni]
Similarity search - Component
Biological speciesStreptomyces seoulensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsWuerges, J. / Lee, J.-W. / Yim, Y.-I. / Yim, H.-S. / Kang, S.-O. / Djinovic Carugo, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of nickel-containing superoxide dismutase reveals another type of active site
Authors: Wuerges, J. / Lee, J.-W. / Yim, Y.-I. / Yim, H.-S. / Kang, S.-O. / Djinovic Carugo, K.
History
DepositionJul 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)160,73740
Polymers158,49512
Non-polymers2,24128
Water27,7071538
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)80,36820
Polymers79,2486
Non-polymers1,12114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16370 Å2
ΔGint-229 kcal/mol
Surface area26330 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)80,36820
Polymers79,2486
Non-polymers1,12114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16160 Å2
ΔGint-209 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.260, 113.749, 128.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a homohexamer which shows a threefold symmetry axis and three twofold symmetry axes in a plane perpendicular to the threefold axis

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Components

#1: Protein
Superoxide dismutase [Ni] / E.C.1.15.1.1 / nickel-containing superoxide dismutase / NiSOD / Ni-containing superoxide dismutase


Mass: 13207.948 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: THE ASYMMETRIC UNIT CONTAINS TWO HEXAMERS / Source: (natural) Streptomyces seoulensis (bacteria) / References: UniProt: P80734, superoxide dismutase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-3NI / NICKEL (III) ION


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


Mass: 18.015 Da / Num. of mol.: 1538 / 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: 2.29 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: ammonium sulfate, 2-propanol, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.2398 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.2→31.1 Å / Num. all: 84100 / Num. obs: 83880 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 5.5 / Num. unique all: 12093 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→31.1 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.167 3400 -random
Rwork0.157 ---
all-84100 --
obs-83880 99.7 %-
Displacement parametersBiso mean: 22.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11172 0 92 1538 12802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcangle_it1.14
X-RAY DIFFRACTIONc_mcbond_it1.7
X-RAY DIFFRACTIONc_scbond_it2.08
X-RAY DIFFRACTIONc_scangle_it2.99

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