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- PDB-4l05: Cu/Zn superoxide dismutase from Brucella abortus -

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Basic information

Entry
Database: PDB / ID: 4l05
TitleCu/Zn superoxide dismutase from Brucella abortus
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / superoxide dismutase / Brucella abortus
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / periplasmic space / metal 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 / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.098 Å
AuthorsShin, D.S. / Didonato, M. / Pratt, A.J. / Bruns, C.K. / Cabelli, D.E. / Kroll, J.S. / Belzer, C.A. / Tabatabai, L.B. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: J.Bacteriol. / Year: 2015
Title: Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus.
Authors: Pratt, A.J. / DiDonato, M. / Shin, D.S. / Cabelli, D.E. / Bruns, C.K. / Belzer, C.A. / Gorringe, A.R. / Langford, P.R. / Tabatabai, L.B. / Kroll, J.S. / Tainer, J.A. / Getzoff, E.D.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionOct 23, 2013ID: 2AQM
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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_alt_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_alt_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.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_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_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 [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4786
Polymers16,0971
Non-polymers3815
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.910, 70.528, 80.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

21A-528-

HOH

31A-558-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 16097.110 Da / Num. of mol.: 1 / Fragment: UNP residues 20-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: sodC, BruAb2_0527 / Production host: Escherichia coli (E. coli) / References: UniProt: P15453, superoxide dismutase

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Non-polymers , 6 types, 267 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 150 mM potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.775 Å
DetectorType: ADSC / Detector: CCD / Date: Jun 23, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.098→30 Å / Num. all: 58063 / Num. obs: 56763 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.55 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.3
Reflection shellResolution: 1.098→1.14 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 4.8 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQW

1eqw


Resolution: 1.098→25.041 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 9.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1183 2833 4.99 %
Rwork0.1134 --
obs0.1137 56760 97.77 %
all-56762 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.098→25.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 14 262 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091230
X-RAY DIFFRACTIONf_angle_d1.3671646
X-RAY DIFFRACTIONf_dihedral_angle_d13.255453
X-RAY DIFFRACTIONf_chiral_restr0.081177
X-RAY DIFFRACTIONf_plane_restr0.007217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0984-1.11740.15521200.15642547X-RAY DIFFRACTION93
1.1174-1.13770.15591370.14632683X-RAY DIFFRACTION97
1.1377-1.15960.14621520.12782635X-RAY DIFFRACTION98
1.1596-1.18320.1351270.12872668X-RAY DIFFRACTION97
1.1832-1.2090.13911170.12472652X-RAY DIFFRACTION97
1.209-1.23710.14741370.12172640X-RAY DIFFRACTION97
1.2371-1.2680.14751190.12042631X-RAY DIFFRACTION96
1.268-1.30230.12191560.11252586X-RAY DIFFRACTION95
1.3023-1.34060.11791470.10992611X-RAY DIFFRACTION95
1.3406-1.38390.10811410.1052619X-RAY DIFFRACTION96
1.3839-1.43330.10711340.10562670X-RAY DIFFRACTION97
1.4333-1.49070.11441460.09952705X-RAY DIFFRACTION98
1.4907-1.55860.10981600.09452717X-RAY DIFFRACTION99
1.5586-1.64070.10391420.09152753X-RAY DIFFRACTION100
1.6407-1.74350.09561460.09412744X-RAY DIFFRACTION100
1.7435-1.87810.10561390.09652774X-RAY DIFFRACTION100
1.8781-2.0670.10231400.09842775X-RAY DIFFRACTION100
2.067-2.36590.10471610.10182801X-RAY DIFFRACTION100
2.3659-2.980.12721590.11632797X-RAY DIFFRACTION100
2.98-25.04760.12471530.13662919X-RAY DIFFRACTION100

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