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- PDB-2a5m: NMR structure of murine gamma-S crystallin from joint refinement ... -

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Basic information

Entry
Database: PDB / ID: 2a5m
TitleNMR structure of murine gamma-S crystallin from joint refinement with SAXS data
ComponentsGamma crystallin S
KeywordsSTRUCTURAL PROTEIN / SAXS / SMALL-ANGLE X-RAY SCATTERING / ALIGNMENT / DEUTERATION / LIQUID CRYSTAL / PF1 / 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 / simulated annealing
AuthorsGrishaev, A. / Wu, J. / Trewhella, J. / Bax, A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data.
Authors: Grishaev, A. / Wu, J. / Trewhella, J. / Bax, A.
#1: Journal: To be Published
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 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 #1closest to the average

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Components

#1: Protein 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 / Plasmid: pET17b / 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: SAXS data was collected on a home-built instrument using a sealed-source X-ray tube and a one-dimensional position sensitive detector. All NMR restraints were taken from entry 1ZWM.

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Sample preparation

DetailsContents: 0.22 mM gamma-S crystallin, 25 mM imidazole, pH 6.0, 10 mM KCl, 0.04% NaN3, 10 mM DTT, for SAXS data. All NMR conditions as reported for 1ZWM
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 25 mM IMIDAZOLE, 10 mM KCL, 0.04% NaN3 / pH: 6 / Pressure: 1 atm / Temperature: 291.4 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 softwareName: CNS / Version: 1.0 with an additional SAXS data fitting module
Developer: BRUNGER,ADAMS,BONVIN,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Experimental NMR data is the same as those in the PDB deposition 1ZWM. SAXS data over the range q = 0.02 to 0.22 A-1 was fitted by an in-house written CNS module.
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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