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- PDB-3f7k: X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxid... -

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Basic information

Entry
Database: PDB / ID: 3f7k
TitleX-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex
ComponentsCopper,Zinc Superoxide Dismutase
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) / superoxide dismutase / Greek key beta-barrel / amyloid filaments / ALS / FALS / Lou Gehrig's disease / amyotrophic lateral sclerosis / Alvinella pompejana / Pompeii worm / eukaryotic thermophile / thermostable protein / hydrogen peroxide product complex
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / copper ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / COPPER (I) ION / HYDROGEN PEROXIDE / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesAlvinella pompejana (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsShin, D.S. / DiDonato, M. / Barondeau, D.P. / Getzoff, E.D. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis.
Authors: Shin, D.S. / Didonato, M. / Barondeau, D.P. / Hura, G.L. / Hitomi, C. / Berglund, J.A. / Getzoff, E.D. / Cary, S.C. / Tainer, J.A.
History
DepositionNov 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMIANTION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper,Zinc Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,35610
Polymers15,7221
Non-polymers6349
Water5,314295
1
A: Copper,Zinc Superoxide Dismutase
hetero molecules

A: Copper,Zinc Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,71220
Polymers31,4452
Non-polymers1,26818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area3560 Å2
ΔGint-144 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.563, 62.563, 163.745
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-206-

SO4

21A-483-

HOH

DetailsThe second subunit of the dimer is generated by the operators y-x,y,1/2-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper,Zinc Superoxide Dismutase


Mass: 15722.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alvinella pompejana (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: B6CHW7*PLUS, superoxide dismutase

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Non-polymers , 7 types, 304 molecules

#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 55% saturated ammonium sulfate, 100 mM Na citrate followed by transfer to 90% saturated ammonium sulfate, 100 mM Na citrate (pH 5.5) and 1 mM hydrogen peroxide, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2004
RadiationMonochromator: SIBYLS KOHZU DUAL DOUBLE SI(111) CRYSTAL MONOCHROMATOR (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 39844 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.055 / Net I/σ(I): 22.62
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.32 / % possible all: 58

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Processing

Software
NameClassification
HKL-2000data collection
XFITdata reduction
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→45 Å / Num. parameters: 13139 / Num. restraintsaints: 15754 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1994 5.011 %RANDOM
all0.147 39789 --
obs0.128 ---
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 1057.75 / Occupancy sum non hydrogen: 1399.38
Refinement stepCycle: LAST / Resolution: 1.35→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 26 295 1459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.054
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.045
X-RAY DIFFRACTIONs_approx_iso_adps0.091

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