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- PDB-1ixb: CRYSTAL STRUCTURE OF THE E. COLI MANGANESE(II) SUPEROXIDE DISMUTA... -

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Basic information

Entry
Database: PDB / ID: 1ixb
TitleCRYSTAL STRUCTURE OF THE E. COLI MANGANESE(II) SUPEROXIDE DISMUTASE MUTANT Y174F AT 0.90 ANGSTROMS RESOLUTION.
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / MANGANESE(II) SUPEROXIDE DISMUTASE / Y174F MUTANT / HYDROGEN BOND REACTIVITY / ULTRAHIGH RESOLUTION
Function / homology
Function and homology information


cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress ...cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress / protein homodimerization activity / DNA binding / metal ion binding / cytosol / cytoplasm
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
MANGANESE ION, 1 HYDROXYL COORDINATED / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsAnderson, B.F. / Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
Citation
Journal: To be Published
Title: Structures at 0.90 A resolution of the oxidised and reduced forms of the Y174F mutant of the manganese superoxide dismutase from Escherichia coli
Authors: Anderson, B.F. / Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
#1: Journal: Biochemistry / Year: 2001
Title: Removing a Hydrogen Bond in the Dimer Interface of Escherichia Coli Manganese Superoxide Dismutase Alters Structure and Reactivity
Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
#2: Journal: Biochemistry / Year: 2001
Title: Outer Sphere Mutations Perturb Metal Reactivity in Manganese Superoxide Dismutase
Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B.
History
DepositionJun 18, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)46,1064
Polymers45,9622
Non-polymers1442
Water16,664925
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-12 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.815, 45.832, 96.187
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUPEROXIDE DISMUTASE / / MnSOD


Mass: 22980.877 Da / Num. of mol.: 2 / Mutation: Y174F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PDT1-5 / Production host: Escherichia coli (E. coli) / Strain (production host): QC781 / References: UniProt: P00448, superoxide dismutase
#2: Chemical ChemComp-MH2 / MANGANESE ION, 1 HYDROXYL COORDINATED / [MN(OH)]+


Mass: 71.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMnO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 925 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16-20% PEG6000, 0.1M BICINE. CRYSTALS WERE REDUCED JUST PRIOR TO FREEZING BY ADDITION OF 10% H2O2 (1 PART to 40 PARTS MOTHER LIQUOR), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 2, 1998
RadiationMonochromator: BENT GERMANIUM SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 0.9→50 Å / Num. all: 274173 / Num. obs: 274173 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 56.8
Reflection shellResolution: 0.9→0.91 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.6 / % possible all: 81.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MN-SOD FROM 1IOH

1ioh


Resolution: 0.9→30 Å / Num. parameters: 39423 / Num. restraintsaints: 47096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS No electron density is observed for a second hydrogen atom on the coordinated solvent species in either chain. Thus, the coordinated solvent ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS No electron density is observed for a second hydrogen atom on the coordinated solvent species in either chain. Thus, the coordinated solvent species is assigned as a hydroxide ion. However, a soft vibrational mode involving a putative second hydrogen atom could render this atom undetectable in difference Fourier maps. THE CLOSE CONTACTS AND POOR GEOMETRY LISTED IN REMARK 500 ARE CAUSED BY PARTIAL OCCUPANCIES AND DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.1264 3300 1.204 %RANDOM SHELL
Rwork0.1107 ---
all0.1109 274173 --
obs0.1109 274039 90.9 %-
Solvent computationSolvent model: P.C.MOEWS & R.H.KRETSINGER, J.MOL.BIOL.91(1975)201-228
Refine analyzeNum. disordered residues: 39 / Occupancy sum hydrogen: 2927 / Occupancy sum non hydrogen: 3990.33
Refinement stepCycle: LAST / Resolution: 0.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 4 925 4183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0298
X-RAY DIFFRACTIONs_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.067

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