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- PDB-1ar4: X-RAY STRUCTURE ANALYSIS OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE... -

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Entry
Database: PDB / ID: 1ar4
TitleX-RAY STRUCTURE ANALYSIS 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 ...: / 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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / 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 / ISOMORPHOUS WITH FE-SOD OF P.SHERMANII / Resolution: 1.9 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: Derived calculations / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,4294
Polymers45,3192
Non-polymers1102
Water8,215456
1
A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules

A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8578
Polymers90,6374
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12420 Å2
ΔGint-54 kcal/mol
Surface area28020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.680, 85.640, 108.850
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
11A-247-

HOH

21B-314-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2036, -0.0003, -0.9791), (0.0035, -1, 0.001), (-0.979, -0.0036, -0.2036)
Vector: 58.3649, 33.0615, 71.7647)

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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 (DSM)
Source: (natural) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / References: UniProt: P80293, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CHARGE OF MANGANESE IS NOT YET KNOWN UNAMBIGUOUSLY. MN REFINED AS MN+3 BUT MN+2 IS ALSO POSSIBLE.

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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: 2.05 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 277 K / Method: microseeding / pH: 6.1
Details: PROTEIN WAS CRYSTALLIZED AT 50MG/ML FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15, 4 DEG C, NUCLEATION INDUCED BY MICROSEEDING FROM CRYSTALS GROWN FROM 14MG/ML PROTEIN, 2.4 M (NH4)2SO4, 50 MM ...Details: PROTEIN WAS CRYSTALLIZED AT 50MG/ML FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15, 4 DEG C, NUCLEATION INDUCED BY MICROSEEDING FROM CRYSTALS GROWN FROM 14MG/ML PROTEIN, 2.4 M (NH4)2SO4, 50 MM KPI, PH 7.4, 4 DEG C., microseeding, temperature 277K
PH range: 6.15 (7.4 for microseeds)
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / 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 HI-STAR / Detector: AREA DETECTOR / Date: Dec 1, 1997 / Details: NO
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→12.8 Å / Num. obs: 26323 / % possible obs: 89.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.042 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.042 / % possible all: 72.3
Reflection
*PLUS
Num. measured all: 81457
Reflection shell
*PLUS
% possible obs: 72.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SAINTdata reduction
CCP4(AGROVATAdata scaling
TRUNCATEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH FE-SOD OF P.SHERMANII
Starting model: FE-SOD OF P.SHERMANII

Resolution: 1.9→9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4.5
Details: MN CENTER REFINED WITHOUT VDW AND DISTANCE RESTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2493 10 %RANDOM
Rwork0.156 ---
obs0.156 24891 84.81 %-
Displacement parametersBiso mean: 15.9 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 2 456 3668
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_deg1.32
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.84
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.92
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: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.246 220 9.5 %
Rwork0.206 2093 -
obs--64.3 %
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_deg21.84
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.92

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