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- PDB-6if9: Solution-state NMR structure of G57W human gammaS crystallin -

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Basic information

Entry
Database: PDB / ID: 6if9
TitleSolution-state NMR structure of G57W human gammaS crystallin
ComponentsGamma-crystallin S
KeywordsRECOMBINATION / STRUCTURE FROM CYANA 3.97
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
Similarity search - Function
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSharma, S. / Bari, K.J. / Chary, K.V.R.
CitationJournal: J. Struct. Biol. / Year: 2019
Title: Structure of G57W mutant of human gamma S-crystallin and its involvement in cataract formation.
Authors: Bari, K.J. / Sharma, S. / Chary, K.V.R.
History
DepositionSep 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)21,1631
Polymers21,1631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9540 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Gamma-crystallin S / Beta-crystallin S / Gamma-S-crystallin


Mass: 21162.936 Da / Num. of mol.: 1 / Mutation: G57W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, CRYG8
Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria)
References: UniProt: P22914

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D C(CO)NH
161isotropic13D H(CCO)NH
171isotropic115N-edited NOESY
181isotropic113C-edited NOESY

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Sample preparation

DetailsType: solution
Contents: 1.5 mM 13C and/or 15N labeled G57W Human GammaS Crystallin, 95% H2O/5% D2O
Label: G57W Human GammaS Crystallin / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.5 mM / Component: G57W Human GammaS Crystallin / Isotopic labeling: 13C and/or 15N labeled
Sample conditionsIonic strength: 25 mM / Label: G57W Human GammaS crystallin / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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