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- PDB-1kkc: Crystal structure of Aspergillus fumigatus MnSOD -

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Basic information

Entry
Database: PDB / ID: 1kkc
TitleCrystal structure of Aspergillus fumigatus MnSOD
ComponentsManganese Superoxide DismutaseSuperoxide dismutase
KeywordsOXIDOREDUCTASE / Homotetramer
Function / homology
Function and homology information


IgE binding / superoxide dismutase / superoxide dismutase activity / manganese ion binding / mitochondrial matrix / mitochondrion / 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], mitochondrial
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFluckiger, S. / Mittl, P.R.E. / Scapozza, L. / Fijten, H. / Folkers, G. / Grutter, M.G. / Blaser, K. / Crameri, R.
CitationJournal: J.Immunol. / Year: 2002
Title: Comparison of the crystal structures of the human manganese superoxide dismutase and the homologous Aspergillus fumigatus allergen at 2-A resolution.
Authors: Fluckiger, S. / Mittl, P.R. / Scapozza, L. / Fijten, H. / Folkers, G. / Grutter, M.G. / Blaser, K. / Crameri, R.
History
DepositionDec 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.4Apr 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: Manganese Superoxide Dismutase
B: Manganese Superoxide Dismutase
X: Manganese Superoxide Dismutase
Y: Manganese Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2868
Polymers98,0674
Non-polymers2204
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-45 kcal/mol
Surface area31480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.882, 98.697, 139.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Manganese Superoxide Dismutase / Superoxide dismutase / MnSOD


Mass: 24516.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q92450, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1dropin water
20.1 mM1dropMgCl2
327 %PEG4001reservoir
4100 mMTris-HCl1reservoirpH8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: Prophysics XRM-216 / Detector: IMAGE PLATE / Date: Jun 23, 2000 / Details: double-focusing mirror system
RadiationMonochromator: ProPhysics MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56622 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / % possible all: 34.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 56585 / Num. measured all: 257369 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 34.8 % / Rmerge(I) obs: 0.333

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2331 5744 RANDOM
Rwork0.1942 --
obs-56538 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.544 Å20 Å20 Å2
2---2.684 Å20 Å2
3---5.228 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 4 745 7059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.1
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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