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- PDB-6pro: MnSOD from Geobacillus stearothermophilus -

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Basic information

Entry
Database: PDB / ID: 6pro
TitleMnSOD from Geobacillus stearothermophilus
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / metal binding / dismutation
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
: / Superoxide dismutase / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.263 Å
AuthorsAdams, J.J. / Morton, C.J. / Parker, M.W.
Citation
Journal: Aust.J.Chem. / Year: 2020
Title: The Crystal Structure of the Manganese Superoxide Dismutase from Geobacillus stearothermophilus: Parker and Blake (1988) Revisited
Authors: Adams, J.J. / Morton, C.J. / Parker, M.W.
#1: Journal: J. Mol. Biol. / Year: 1988
Title: Crystal structure of manganese superoxide dismutase from Bacillus stearothermophilus at 2.4 A resolution.
Authors: Parker, M.W. / Blake, C.C.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3664
Polymers45,2562
Non-polymers1102
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-13 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.200, 111.100, 51.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Superoxide dismutase /


Mass: 22628.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria)
References: UniProt: A0A087LE79, UniProt: P00449*PLUS, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 25-30% PEG6000, 50 mM imidazole / PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room Temperature / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5406 Å
DetectorType: hilger and watts / Detector: DIFFRACTOMETER / Date: Feb 2, 1981
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.26→39.05 Å / Num. obs: 16562 / % possible obs: 83.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.3
Reflection shellResolution: 2.26→2.87 Å / Num. unique obs: 6730 / % possible all: 67.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
in-housedata scaling
in-housephasing
RefinementMethod to determine structure: MIR / Resolution: 2.263→39.049 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 783 4.73 %
Rwork0.1538 15777 -
obs0.1559 16560 83.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.68 Å2 / Biso mean: 34.2176 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: final / Resolution: 2.263→39.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 2 146 3352
Biso mean--11.25 30.74 -
Num. residues----404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.263-2.40470.374760.230753754317
2.4047-2.59040.24751300.20282748287888
2.5904-2.8510.24811550.18812996315196
2.851-3.26340.23961550.171931083263100
3.2634-4.11080.17081630.135931473310100
4.1108-39.05480.15851740.12523241341598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4874-0.2031-0.32171.70770.06292.3231-0.0134-0.07160.1138-0.0032-0.00190.0254-0.0567-0.1040.01070.1-0.0032-0.0090.0957-0.0020.116558.319441.435726.8232
21.378-0.4336-0.26492.2098-0.33712.32770.05990.2048-0.2098-0.2246-0.07970.20.1676-0.21540.00170.10840.0009-0.03750.1657-0.04880.176960.542216.95599.3608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 202)A1 - 202
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 202)B1 - 202

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