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- PDB-1oaj: Active site copper and zinc ions modulate the quaternary structur... -

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Basic information

Entry
Database: PDB / ID: 1oaj
TitleActive site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / PROKARIOTIC CU / ZN SUPEROXIDE DISMUTASE / SUBUNIT INTERACTION RECOGNITION / PROTEIN ELECTROSTATIC
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / periplasmic space / copper ion binding / extracellular space
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 / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesPHOTOBACTERIUM LEIOGNATHI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.73 Å
AuthorsCioni, P. / Pesce, A. / Rocca, B.M.D. / Castelli, S. / Falconi, M. / Parrilli, L. / Bolognesi, M. / Strambini, G. / Desideri, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Active-Site Copper and Zinc Ions Modulate the Quaternary Structure of Prokaryotic Cu,Zn Superoxide Dismutase
Authors: Cioni, P. / Pesce, A. / Morozzo Della Rocca, B. / Castelli, S. / Falconi, M. / Parrilli, L. / Bolognesi, M. / Strambini, G. / Desideri, A.
History
DepositionJan 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_biol
Item: _atom_site.occupancy / _exptl_crystal_grow.method ..._atom_site.occupancy / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9293
Polymers15,8001
Non-polymers1292
Water1,63991
1
A: SUPEROXIDE DISMUTASE
hetero molecules

A: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8576
Polymers31,6002
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)85.900, 85.900, 98.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2021-

HOH

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Components

#1: Protein SUPEROXIDE DISMUTASE /


Mass: 15799.761 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHOTOBACTERIUM LEIOGNATHI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 71/18 / References: UniProt: P00446, superoxide dismutase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMUTATED RESIDUES: LYS 25 ASP
Sequence detailsTHE PROTEIN USED IS A TRUNCATED FORM, WITHOUT THE FIRST 22 RESIDUES SIGNAL SEQUENCE

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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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG 8,000 25%, NACL 100 MM, SODIUM ACETATE 50 MM, PH 4, TEMPERATURE 28C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 14997 / % possible obs: 97.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 20
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 5 / % possible all: 75.8

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.73→30 Å / SU ML: 0.085 / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1499 10 %RANDOM
Rwork0.183 ---
obs0.191 14997 97.5 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.73→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 2 91 1201

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