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- PDB-7svs: Crystal structure analysis of the G73A mutant of Superoxide Dismu... -

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Basic information

Entry
Database: PDB / ID: 7svs
TitleCrystal structure analysis of the G73A mutant of Superoxide Dismutase from Trichoderma reesei
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / enzymatic activity
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
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMendoza Rengifo, E. / Ferreira Jr., J.R. / Garratt, C.R.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/01855-2 Brazil
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Unexpected plasticity of the quaternary structure of iron-manganese superoxide dismutases.
Authors: Mendoza Rengifo, E. / Stelmastchuk Benassi Fontolan, L. / Ribamar Ferreira-Junior, J. / Bleicher, L. / Penner-Hahn, J. / Charles Garratt, R.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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

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
G: Superoxide dismutase
H: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,63416
Polymers186,1948
Non-polymers4408
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-106 kcal/mol
Surface area63780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.170, 110.620, 180.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Superoxide dismutase /


Mass: 23274.311 Da / Num. of mol.: 8 / Mutation: G73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain QM6a) (fungus)
Strain: QM6a / Gene: TRIREDRAFT_66345 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RQS7, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 25% polyethylene glycol (PEG) 3350, 0.1 mM Bis-Tris, pH 5.7
PH range: 5.2-8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→95.17 Å / Num. all: 47807 / Num. obs: 47807 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 45.21 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.083 / Rrim(I) all: 0.212 / Rsym value: 0.195 / Net I/σ(I): 10.1 / Num. measured all: 313253
Reflection shell

Diffraction-ID: 1 / Resolution: 2.8→2.95 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
6.60.94968400.6140.0250.0590.053100
5.70.05316640.9950.0270.0690.06399.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kkc

1kkc


Resolution: 2.8→72.14 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 2402 5.03 %
Rwork0.1903 45315 -
obs0.1937 47717 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.73 Å2 / Biso mean: 40.5433 Å2 / Biso min: 21.55 Å2
Refinement stepCycle: final / Resolution: 2.8→72.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12130 0 8 75 12213
Biso mean--26.24 28.42 -
Num. residues----1562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.8-2.860.39151220.2942606
2.86-2.920.34281490.27192636
2.92-2.990.35121480.25632625
2.99-3.060.34391600.2552624
3.06-3.140.27961180.24132634
3.14-3.240.30311310.2312662
3.24-3.340.29291400.22532626
3.34-3.460.31941450.22672642
3.46-3.60.27271440.22552644
3.6-3.760.28971600.19862624
3.76-3.960.24631460.17792676
3.96-4.210.22291310.15712655
4.21-4.540.22321190.15162721
4.54-4.990.20441630.14472656
4.99-5.710.22441500.15872693
5.71-7.20.22881360.16982744
Refinement TLS params.Method: refined / Origin x: -3.2166 Å / Origin y: 110.2512 Å / Origin z: -1.8342 Å
111213212223313233
T0.2489 Å2-0.053 Å20.0114 Å2-0.2478 Å20.0087 Å2--0.2822 Å2
L0.2961 °2-0.0739 °20.0778 °2-0.2321 °2-0.0037 °2--0.2945 °2
S0.0413 Å °0.0046 Å °-0.0031 Å °-0.0579 Å °-0.0269 Å °0.0497 Å °0.0383 Å °0.03 Å °-0.0159 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 198
2X-RAY DIFFRACTION1allB5 - 198
3X-RAY DIFFRACTION1allC3 - 204
4X-RAY DIFFRACTION1allD6 - 198
5X-RAY DIFFRACTION1allE5 - 198
6X-RAY DIFFRACTION1allF6 - 198
7X-RAY DIFFRACTION1allG7 - 200
8X-RAY DIFFRACTION1allH3 - 198
9X-RAY DIFFRACTION1allJ1 - 80
10X-RAY DIFFRACTION1allI1 - 8

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