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- PDB-1eqw: CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM CU,ZN SUPEROXIDE DISMUTASE -

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Basic information

Entry
Database: PDB / ID: 1eqw
TitleCRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM CU,ZN SUPEROXIDE DISMUTASE
ComponentsCU,ZN SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / superoxide dismutase / Greek key b-barrel
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / periplasmic space / copper ion binding / metal ion binding / identical protein binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / 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] 1 / Superoxide dismutase [Cu-Zn] 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPesce, A. / Battistoni, A. / Stroppolo, M.E. / Polizio, F. / Nardini, M. / Kroll, J.S. / Langford, P.R. / O'Neill, P. / Sette, M. / Desideri, A. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Functional and crystallographic characterization of Salmonella typhimurium Cu,Zn superoxide dismutase coded by the sodCI virulence gene.
Authors: Pesce, A. / Battistoni, A. / Stroppolo, M.E. / Polizio, F. / Nardini, M. / Kroll, J.S. / Langford, P.R. / O'Neill, P. / Sette, M. / Desideri, A. / Bolognesi, M.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _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: CU,ZN SUPEROXIDE DISMUTASE
B: CU,ZN SUPEROXIDE DISMUTASE
C: CU,ZN SUPEROXIDE DISMUTASE
D: CU,ZN SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,46612
Polymers64,9504
Non-polymers5168
Water3,207178
1
A: CU,ZN SUPEROXIDE DISMUTASE
C: CU,ZN SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7336
Polymers32,4752
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-13 kcal/mol
Surface area13300 Å2
MethodPISA
2
B: CU,ZN SUPEROXIDE DISMUTASE
D: CU,ZN SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7336
Polymers32,4752
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.140, 40.659, 114.254
Angle α, β, γ (deg.)90, 107.73, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CU,ZN SUPEROXIDE DISMUTASE


Mass: 16237.467 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P53636, UniProt: P0CW86*PLUS, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8000, sodium chloride, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 %(w/v)PEG80001reservoir
3100 mM1reservoirNaCl
450 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→22.6 Å / Num. all: 27119 / Num. obs: 27119 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.356 / Num. unique all: 1302
Reflection
*PLUS
Num. measured all: 255605
Reflection shell
*PLUS
% possible obs: 93.2 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.3→22.6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2712 -random
Rwork0.226 ---
all0.226 27119 --
obs0.226 27119 96.2 %-
Refinement stepCycle: LAST / Resolution: 2.3→22.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4445 0 8 178 4631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_bond_d0.006
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 22.6 Å / Num. reflection obs: 24407 / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43 Å2

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