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- PDB-2m3c: Solution Structure of gammaM7-Crystallin -

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Basic information

Entry
Database: PDB / ID: 2m3c
TitleSolution Structure of gammaM7-Crystallin
ComponentsCrystallin, gamma M7
KeywordsSTRUCTURAL PROTEIN / beta/gamma crystallin / fish lens
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
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
Crystallin, gamma M7
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 14
AuthorsMahler, B. / Wu, Z.
CitationJournal: Biochemistry / Year: 2013
Title: Structure and Dynamics of the Fish Eye Lens Protein, gamma M7-Crystallin.
Authors: Mahler, B. / Chen, Y. / Ford, J. / Thiel, C. / Wistow, G. / Wu, Z.
History
DepositionJan 16, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.3May 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: Crystallin, gamma M7


Theoretical massNumber of molelcules
Total (without water)20,9381
Polymers20,9381
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Crystallin, gamma M7 / / GammaM7-crystallin / Uncharacterized protein


Mass: 20937.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: crygm7, DKEY-57A22.1-001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q5XTN3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited NOESY-HSQC
1213D 13C-edited HMQC-NOESY-HMQC
131RDC by HSQC-TROSY
1413D HNCA
1513D CBCA(CO)NH

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Sample preparation

DetailsContents: 25 mM [U-2H] imidazole, 20 mM potassium chloride, 2 mM DTT, 0.04 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMimidazole[U-2H]1
20 mMpotassium chloride1
2 mMDTT1
0.04 %sodium azide1
Sample conditionsIonic strength: 20 / pH: 6.2 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
AQUARullmann, Doreleijers and Kapteinrefinement
ProcheckNMRLaskowski and MacArthurrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
XwinNMRBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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