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- PDB-1ar5: X-RAY STRUCTURE OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PRO... -

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Basic information

Entry
Database: PDB / ID: 1ar5
TitleX-RAY STRUCTURE OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PROPIONIBACTERIUM SHERMANII ACTIVE WITH FE OR MN
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / DEGRADES O2- / DISMUTASE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn/Fe]
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement/MIR / Resolution: 1.6 Å
AuthorsSchmidt, M. / Meier, B. / Parak, F.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1996
Title: X-Ray Structure of the Cambialistic Superoxide Dismutase from Propionibacterium Shermanii Active with Fe or Mn
Authors: Schmidt, M. / Meier, B. / Parak, F.
History
DepositionAug 9, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4304
Polymers45,3192
Non-polymers1122
Water8,125451
1
A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules

A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8618
Polymers90,6374
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)79.830, 85.687, 108.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-353-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.1993, -0.002, -0.9799), (0.0033, -1, 0.0028), (-0.9799, -0.0038, -0.1993)
Vector: 58.4946, 33.0289, 71.6907)

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Components

#1: Protein SUPEROXIDE DISMUTASE / / SOD


Mass: 22659.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS
Source: (natural) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / References: UniProt: P80293, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.04 Å3/Da / Density % sol: 32.2 % / Description: COMBINATION OF MR AND MIR
Crystal growTemperature: 277 K / Method: microseeding / pH: 6.15
Details: PROTEIN WAS CRYSTALLIZED FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15 AT 4 DEG C. NUCLEATION WAS INDUCED BY ADDING A MICROSEED FROM CRYSTALS GROWN FROM 2.4 M (NH4)2SO4, 50MM KPI, PH 7.4 AT 4 ...Details: PROTEIN WAS CRYSTALLIZED FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15 AT 4 DEG C. NUCLEATION WAS INDUCED BY ADDING A MICROSEED FROM CRYSTALS GROWN FROM 2.4 M (NH4)2SO4, 50MM KPI, PH 7.4 AT 4 DEG C., microseeding, temperature 277K
PH range: 6.15 (7.4 for microseeds)
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
22.15 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→39.8 Å / Num. obs: 47484 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 15.01 Å2 / Rmerge(I) obs: 0.027 / Rsym value: 0.027 / Net I/σ(I): 22.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 7 / Rsym value: 0.136 / % possible all: 90.2
Reflection
*PLUS
% possible obs: 85.6 % / Num. measured all: 119504 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SAINTdata reduction
Agrovatadata scaling
TRUNCATEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: molecular replacement/MIR
Starting model: FE-SOD E.COLI, MN-SOD T.THERMOPHILUS

Resolution: 1.6→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4.5
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4451 10 %RANDOM
Rwork0.163 ---
obs0.163 44130 89.79 %-
Displacement parametersBiso mean: 16.83 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 2 451 3663
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.291
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.913
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2099 409 9.2 %
Rwork0.2044 4059 -
obs--73.42 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.006
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.913

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