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- PDB-2m3t: Solution-state NMR structure of wild-type human gamma(S)-crystallin -

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Basic information

Entry
Database: PDB / ID: 2m3t
TitleSolution-state NMR structure of wild-type human gamma(S)-crystallin
ComponentsBeta-crystallin S
KeywordsSTRUCTURAL PROTEIN / gamma-S / eye lens / aggregation / crystallin / cataract / CRYGS
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
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsBrubaker, W.D. / Martin, R.W.
CitationJournal: Structure / Year: 2013
Title: Preferential and Specific Binding of Human alpha B-Crystallin to a Cataract-Related Variant of gamma S-Crystallin.
Authors: Kingsley, C.N. / Brubaker, W.D. / Markovic, S. / Diehl, A. / Brindley, A.J. / Oschkinat, H. / Martin, R.W.
History
DepositionJan 25, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 20959.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, GRYG8 / Variant: Wild-Type / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P22914

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1423D HN(CA)CB
1523D CBCA(CO)NH
1623D HNCO
1723D (H)CCH-TOCSY
1823D (H)CCH-COSY
1923D 1H-15N NOESY
11023D 1H-13C NOESY aliphatic
11123D 1H-13C NOESY aromatic
21212D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM acetic acid, 2 mM 2,2',3,3'-D4 TSP, 0.05 % sodium azide, 7.5 % DIOTPC, 2.5 % DIOHPC, 2 mM [U-15N] (gamma)S-WT, 90% H2O/10% D2O90% H2O/10% D2O
210 mM acetic acid, 2 mM 2,2',3,3'-D4 TSP, 0.05 % sodium azide, 2.11 mM [U-13C; U-15N] (gamma)S-WT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMacetic acid-11
2 mMTSP-22,2',3,3'-D41
0.05 %sodium azide-31
7.5 %DIOTPC-41
2.5 %DIOHPC-51
2 mM(gamma)S-WT-6[U-15N]1
10 mMacetic acid-72
2 mMTSP-82,2',3,3'-D42
0.05 %sodium azide-92
2.11 mM(gamma)S-WT-10[U-13C; U-15N]2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
14.5 ambient 295 K
24.5 ambient 305 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
VNMRVariancollection
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 7444 / NOE intraresidue total count: 1547 / NOE long range total count: 3052 / NOE medium range total count: 1286 / NOE sequential total count: 1559
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 21

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