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- PDB-1bt8: P.SHERMANII SOD(FE+3) PH 10.0 -

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Basic information

Entry
Database: PDB / ID: 1bt8
TitleP.SHERMANII SOD(FE+3) PH 10.0
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / SUPEROXIDE 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 / Resolution: 1.85 Å
AuthorsSchmidt, M.
CitationJournal: Eur.J.Biochem. / Year: 1999
Title: Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH-value A crystallographic analysis
Authors: Schmidt, M.
History
DepositionSep 1, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: 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 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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

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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
Water4,936274
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
Buried area12490 Å2
ΔGint-86 kcal/mol
Surface area28620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.689, 87.293, 110.841
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-312-

HOH

21A-314-

HOH

31B-262-

HOH

41B-269-

HOH

51B-274-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4338, 0.0029, -0.901), (0.0004, -1, -0.003), (-0.901, 0.0009, -0.4338)
Vector: 47.2006, 32.2657, 75.2082)

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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
Source: (natural) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Cellular location: CYTOPLASM / Species: Propionibacterium freudenreichii / Strain: PZ3 / 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.: 274 / 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 Å3/Da / Density % sol: 32 %
Crystal growpH: 10 / Details: pH 10.0
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
350 mMpotassium phosphate1reservoir
4ammonium sulfate1reservoir

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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: May 1, 1998
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→40.2 Å / Num. obs: 22958 / % possible obs: 70.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 15.4
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.147 / % possible all: 57.2
Reflection
*PLUS
Num. obs: 22966 / % possible obs: 71 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 57.2 % / Rmerge(I) obs: 0.147

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
SAINTdata reduction
SAINTdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AR5

1ar5


Resolution: 1.85→8.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.5
Details: IRON AND COORDINATED SOLVENT MOLECULES REFINED UNRESTRAINED THE IRON IONS AND THE COORDINATING SOLVENT MOLECULES WERE REFINED WITHOUT RESTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1140 5.1 %RANDOM
Rwork0.176 ---
obs0.176 22422 68.9 %-
Displacement parametersBiso mean: 17.2 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.85→8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 2 274 3484
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
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_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.881.5
X-RAY DIFFRACTIONx_mcangle_it2.762
X-RAY DIFFRACTIONx_scbond_it3.292
X-RAY DIFFRACTIONx_scangle_it4.592.5
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.277 118 5.4 %
Rwork0.247 2050 -
obs--54.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174 / Rfactor Rfree: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85

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