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- PDB-1ma1: Structure and properties of the atypical iron superoxide dismutas... -

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Basic information

Entry
Database: PDB / ID: 1ma1
TitleStructure and properties of the atypical iron superoxide dismutase from Methanobacterium thermoautotrophicum
Componentssuperoxide dismutase
KeywordsOXIDOREDUCTASE / iron superoxide dismutase / metal specificity / azide inhibition / peroxide inactivation
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
: / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAdams, J.J. / Anderson, B.F. / Renault, J.P. / Verchere-Beaur, C. / Morgenstern-Badarau, I. / Jameson, G.B.
CitationJournal: To be published
Title: Structure and properties of the atypical iron superoxide dismutase from Methanobacterium thermoautotrophicum
Authors: Adams, J.J. / Anderson, B.F. / Renault, J.P. / Verchere-Beaur, C. / Morgenstern-Badarau, I. / Jameson, G.B.
History
DepositionJul 31, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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
C: superoxide dismutase
D: superoxide dismutase
E: superoxide dismutase
F: superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,11012
Polymers144,7756
Non-polymers3356
Water7,602422
1
A: superoxide dismutase
B: superoxide dismutase
hetero molecules

A: superoxide dismutase
B: superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7408
Polymers96,5174
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
C: superoxide dismutase
D: superoxide dismutase
E: superoxide dismutase
F: superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7408
Polymers96,5174
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14970 Å2
ΔGint-21 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.619, 114.082, 58.087
Angle α, β, γ (deg.)90.00, 94.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
superoxide dismutase


Mass: 24129.191 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: SODF / Plasmid: pETS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE1) / References: UniProt: P18868, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, sodium azide, feric chloride, amonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 19, 2001 / Details: AXCO SRA/PX50, confocal monocapillary optic
RadiationMonochromator: glass monocapillary optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 34876 / Num. obs: 34876 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 34.92 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.25
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3754 / % possible all: 93.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SSS

1sss
PDB Unreleased entry


Resolution: 2.6→50 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1725 -RANDOM
Rwork0.2149 ---
all0.217 37537 --
obs0.217 34876 92.9 %-
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.19 Å2-9.19 Å21.99 Å2
2--0 Å25.82 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 3 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10032 0 12 416 10460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.329 166 -
Rwork0.29 --
obs-3471 93.6 %

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