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- PDB-1bs3: P.SHERMANII SOD(FE+3) FLUORIDE -

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Basic information

Entry
Database: PDB / ID: 1bs3
TitleP.SHERMANII SOD(FE+3) FLUORIDE
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / FLUORIDE
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
FLUORIDE ION / : / Superoxide dismutase [Mn/Fe]
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.55 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
DepositionAug 31, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 28, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)45,4686
Polymers45,3192
Non-polymers1504
Water8,611478
1
A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules

A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,93712
Polymers90,6374
Non-polymers2998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12490 Å2
ΔGint-59 kcal/mol
Surface area27790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.420, 85.280, 108.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2028, -0.0019, -0.9792), (0.0036, -1, 0.0027), (-0.9792, -0.004, -0.2028)
Vector: 58.1922, 32.9142, 71.5343)

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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: COMPETITIVELY INHIBITED BY FLOURIDE. FLUORIDE OCCUPIES SUBSTRATE BINDING SITE.
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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 6.1 / Details: pH 6.1
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
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: Sep 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→39.7 Å / Num. obs: 45799 / % possible obs: 83.1 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.034 / Net I/σ(I): 18
Reflection shellResolution: 1.55→1.62 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 7.6 / Rsym value: 0.148 / % possible all: 67
Reflection
*PLUS
Num. obs: 45923 / % possible obs: 78 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.036

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
SAINTdata reduction
SAINTdata scaling
X-PLOR3.851phasing
RefinementStarting model: PDB ENTRY 1AR5

1ar5


Resolution: 1.55→9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.5 / Details: IRON AND FLUORIDE REFINED UNRESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4178 10 %RANDOM
Rwork0.174 ---
obs0.174 41693 78.2 %-
Displacement parametersBiso mean: 14.1 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.55→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 4 478 3690
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.88
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it11.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it2.22
X-RAY DIFFRACTIONx_scangle_it3.32.5
LS refinement shellResolution: 1.55→1.62 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.241 439 10.6 %
Rwork0.233 3691 -
obs--62.1 %
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: 0.17 / Rfactor Rfree: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.88

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