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- PDB-1zlz: Re-Evaluation of the Low-Temperature Azide in Mn-Dependent Supero... -

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Basic information

Entry
Database: PDB / ID: 1zlz
TitleRe-Evaluation of the Low-Temperature Azide in Mn-Dependent Superoxide Dismutase
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / Azide derivative / manganese superoxide dismutase / localized mixed-valent dimer
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
AZIDE ION / MANGANESE ION, 1 HYDROXYL COORDINATED / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSalvador, J.R. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B.
CitationJournal: TO BE PUBLISHED
Title: Azide Adduct of the Y174F mutant of Manganese superoxide dismutase from Escherichia coli
Authors: Salvador, J.R. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B.
History
DepositionMay 9, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.5Oct 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)46,1906
Polymers45,9622
Non-polymers2284
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-12 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.727, 45.676, 95.859
Angle α, β, γ (deg.)90.00, 97.92, 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-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-MH2 / MANGANESE ION, 1 HYDROXYL COORDINATED / [MN(OH)]+


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


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 6000, MPD, TRIS buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 13, 2005 / Details: Osmic blue
RadiationMonochromator: Osmic blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→35.69 Å / Num. all: 56272 / Num. obs: 52079 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.02 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.1
Reflection shellResolution: 1.546→1.586 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.9 / % possible all: 65

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Processing

Software
NameVersionClassification
SHELXL-97refinement
CrystalClear(MSC/RIGAKU)data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1IX9

1ix9


Resolution: 1.55→35.69 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflectionSelection details
Rfree0.22193 2848 Random
Rwork0.1804 --
all0.1859 56727 -
obs0.1817 52049 -
Displacement parametersBiso mean: 12.811 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 10 421 3751
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d1.34
X-RAY DIFFRACTIONs_bond_d0.011

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