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- PDB-1zwm: NMR structure of murine gamma-S crystallin -

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Basic information

Entry
Database: PDB / ID: 1zwm
TitleNMR structure of murine gamma-S crystallin
ComponentsGamma crystallin S
KeywordsSTRUCTURAL PROTEIN / alignment / deuteration / liquid crystal / Pf1 / relaxation / RDC / residual dipolar coupling / molecular fragment replacement / MFR
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / MFR, simulated annealing
AuthorsWu, Z. / Delaglio, F. / Wyatt, K. / Wistow, G. / Bax, A.
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of (gamma)S-crystallin by molecular fragment replacement NMR.
Authors: Wu, Z. / Delaglio, F. / Wyatt, K. / Wistow, G. / Bax, A.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)20,7471
Polymers20,7471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #12closest to the average

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Components

#1: Protein Gamma crystallin S / Gamma crystallin S


Mass: 20747.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crygs / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O35486

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.7-1.5 mM gS, 25 mM imidazole, pH 6.0, 10 mM KCl, 0.04% NaN3. Dipolar couplings measured in 2H/15N/13C gammaS, in stretched polyacrylamide gel, and in 3 mg/mL Pf1 (gelled), 120 mM KCl; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 25 mM imidazole, 10 mM KCl, 0.04% NaN3 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX600 with PFG cryoprobe / Manufacturer: Bruker / Model: DRX600 with PFG cryoprobe / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglio, Grzesiek, Zhu, Vuister, Pfeifer, Baxdata analysis
DYNAMO3.1Delaglio, Kuszewskirefinement
X-PLOR2.9.4Brunger, Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: MFR, simulated annealing / Software ordinal: 1
Details: simulated annealing, including a H-bond potential of mean force, H-bond pairing was determined automatically, no explicit H-bond pairing restraints were used; tight backbone torsion angle ...Details: simulated annealing, including a H-bond potential of mean force, H-bond pairing was determined automatically, no explicit H-bond pairing restraints were used; tight backbone torsion angle restraints are derived from a search through the RCSB for fragments that match experimental dipolar couplings
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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