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- PDB-7cjw: Solution structure of monomeric superoxide dismutase 1 with an ad... -

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Basic information

Entry
Database: PDB / ID: 7cjw
TitleSolution structure of monomeric superoxide dismutase 1 with an additional mutation H46W in a crowded environment
ComponentsMonomeric Human Cu,Zn Superoxide dismutase
KeywordsOXIDOREDUCTASE / Dismutase / Monomer / Amyloid
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsIwakawa, N. / Morimoto, D. / Walinda, E. / Danielsson, J. / Shirakawa, M. / Sugase, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP18J22192 Japan
Japan Society for the Promotion of ScienceJP17K19196 Japan
Japan Society for the Promotion of ScienceJP18H04551 Japan
CitationJournal: J.Phys.Chem.B / Year: 2021
Title: Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 beta-Barrel.
Authors: Iwakawa, N. / Morimoto, D. / Walinda, E. / Leeb, S. / Shirakawa, M. / Danielsson, J. / Sugase, K.
History
DepositionJul 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monomeric Human Cu,Zn Superoxide dismutase


Theoretical massNumber of molelcules
Total (without water)11,0381
Polymers11,0381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6250 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1target function

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Components

#1: Protein Monomeric Human Cu,Zn Superoxide dismutase


Mass: 11038.354 Da / Num. of mol.: 1 / Mutation: H46W
Source method: isolated from a genetically manipulated source
Details: loops IV and VII deleted, apo form / Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: superoxide dismutase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC aliphatic
1211isotropic12D 1H-13C HSQC aromatic
1201isotropic13D HNCO
1191isotropic13D HN(CA)CO
1181isotropic13D HNCA
1171isotropic13D HN(CO)CA
1161isotropic13D CBCA(CO)NH
1151isotropic13D HN(CA)CB
1141isotropic13D CC(CO)NH
1131isotropic13D (H)CCH-COSY
1121isotropic13D (H)CCH-TOCSY
1111isotropic13D H(CCO)NH
1101isotropic12D (HB)CB(CGCD)HD
191isotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, with an additional mutation H46W, 10 mM Bis-Tris, 50 mg/mL Lysozyme from Egg White, 95% H2O/5% D2O
Label: 13C/15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, with an additional mutation H46W[U-13C; U-15N]1
10 mMBis-Trisnatural abundance1
50 mg/mLLysozyme from Egg Whitenatural abundance1
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
NMRPipe9.6Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxstructure calculation
CcpNmr Analysis2.4.2CCPNdata analysis
MOLMOL2K.2Koradi, Billeter and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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