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- PDB-2nbr: The Solution Structure of Human gammaC-crystallin -

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Basic information

Entry
Database: PDB / ID: 2nbr
TitleThe Solution Structure of Human gammaC-crystallin
ComponentsGamma-crystallin C
KeywordsSTRUCTURAL PROTEIN / Human gammaC-crystallin
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / nucleus / cytoplasm
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
Model detailslowest energy, model1
AuthorsDixit, K. / Pande, A. / Pande, J. / Sarma, S.P.
CitationJournal: Biochemistry / Year: 2016
Title: Nuclear Magnetic Resonance Structure of a Major Lens Protein, Human gamma C-Crystallin: Role of the Dipole Moment in Protein Solubility.
Authors: Dixit, K. / Pande, A. / Pande, J. / Sarma, S.P.
History
DepositionMar 12, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 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 1.3May 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: Gamma-crystallin C


Theoretical massNumber of molelcules
Total (without water)20,7741
Polymers20,7741
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Gamma-crystallin C / Gamma-C-crystallin / Gamma-crystallin 2-1 / Gamma-crystallin 3


Mass: 20774.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGC, CRYG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07315

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
122Expt 10 (H{[N]+[HA]})
1313D HNHB
1413D HNCO
1513D HN(CA)CB
161Expt 16 (H[N[co[{CA|ca[C]}]]])
171Expt 21 (C coNH.relayed)
1913D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] Molecule 1-1, 20 mM potassium phosphate-2, 5 mM DTT-3, 20 mM sodium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-15N] Molecule 1-5, 20 mM potassium phosphate-6, 5 mM DTT-7, 20 mM sodium chloride-8, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-99% 13C; U-99% 15N] Molecule 1-9, 20 mM potassium phosphate-10, 5 mM DTT-11, 20 mM sodium chloride-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMolecule 1-1[U-99% 13C; U-99% 15N]1
20 mMpotassium phosphate-21
5 mMDTT-31
20 mMsodium chloride-41
0.5 mMMolecule 1-5[U-15N]2
20 mMpotassium phosphate-62
5 mMDTT-72
20 mMsodium chloride-82
0.5 mMMolecule 1-9[U-99% 13C; U-99% 15N]3
20 mMpotassium phosphate-103
5 mMDTT-113
20 mMsodium chloride-123
Sample conditionsIonic strength: 0.02 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DDS2AgilentDDS26001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.1CCPNchemical shift assignment
NMRDrawanyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectrum display
NMRDrawanyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectrum analysis
NMRPipeanyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectrum processing
NMRViewanyJohnson, One Moon Scientific, Guntert, Mumenthaler and Wuthrichspectrum display
NMRViewanyJohnson, One Moon Scientific, Guntert, Mumenthaler and Wuthrichspectrum analysis
NMRViewanyJohnson, One Moon Scientific, Guntert, Mumenthaler and Wuthrichstructure solution
NMRViewanyJohnson, One Moon Scientific, Guntert, Mumenthaler and Wuthrichspectrum display
NMRViewanyJohnson, One Moon Scientific, Guntert, Mumenthaler and Wuthrichspectrum analysis
NMRViewanyJohnson, One Moon Scientific, Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMR constraintsNOE constraints total: 1960 / NOE intraresidue total count: 594 / NOE long range total count: 589 / NOE medium range total count: 148 / NOE sequential total count: 629 / Protein chi angle constraints total count: 114 / Protein phi angle constraints total count: 164 / Protein psi angle constraints total count: 164
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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