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- PDB-2klj: Solution Structure of gammaD-Crystallin with RDC and SAXS -

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Basic information

Entry
Database: PDB / ID: 2klj
TitleSolution Structure of gammaD-Crystallin with RDC and SAXS
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / gammaD-Crystallin / 3D structure / RDC / SAXS / Cataract / Disease mutation / Eye lens protein / Oxidation / Polymorphism / Sensory transduction / Vision
Function / homology
Function and homology information


lens fiber cell differentiation / structural constituent of eye lens / lens development in camera-type eye / visual perception / cellular response to reactive oxygen species / nucleus / cytoplasm
Similarity search - Function
Beta/Gamma crystallin / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWang, J. / Zuo, X. / Yu, P. / Byeon, I. / Jung, J. / Gronenborn, A.M. / Wang, Y.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: Determination of multicomponent protein structures in solution using global orientation and shape restraints.
Authors: Wang, J. / Zuo, X. / Yu, P. / Byeon, I.J. / Jung, J. / Wang, X. / Dyba, M. / Seifert, S. / Schwieters, C.D. / Qin, J. / Gronenborn, A.M. / Wang, Y.X.
#1: Journal: Biochemistry / Year: 2009
Title: The Structure of the Cataract-Causing P23T Mutant of HgD Crystallin Exhibits Distinctive Local Conformational and Dynamic Changes
Authors: Jung, J. / Byeon, I.L. / Wang, Y. / King, J. / Gronenborn, A.M.
History
DepositionJul 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,7671
Polymers20,7671
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Gamma-crystallin D / Gamma-D-crystallin / Gamma-crystallin 4


Mass: 20767.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli (E. coli) / References: UniProt: P07320

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Experimental details

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Experiment

Experiment
Method
SOLUTION SCATTERING
SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM entity-1, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-100% 15N] entity-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMentity-11
0.8 mMentity-2[U-100% 15N]2
Sample conditionsIonic strength: 0.02 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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Data collection

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz
Soln scatterType: x-ray / Buffer name: 20 MM NACL 20 MM MES 5 MM DTT / Conc. range: 1.0-3.6 / Data analysis software list: GNOM
Data reduction software list: MARDETECTOR, HOME- WRITTEN PROGRAM
Detector specific: HOME-MADE / Detector type: CCD CAMERA / Mean guiner radius: 1.72 nm / Mean guiner radius esd: 0.03 nm / Num. of time frames: 20 / Protein length: 0.5 / Sample pH: 6.2 / Source beamline: 12-ID / Source class: Y / Source type: APS ARGONNE / Temperature: 298 K

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Processing

NMR softwareName: X-PLOR NIH / Version: 2.22 / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
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: 10
Soln scatter modelConformer selection criteria: STRUCTURES WITH THE LOWEST ENERGY
Num. of conformers calculated: 100 / Num. of conformers submitted: 10 / Representative conformer: 1 / Software list: GNOM

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