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- PDB-2kfb: The structure of the cataract causing P23T mutant of human gamma-... -

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Basic information

Entry
Database: PDB / ID: 2kfb
TitleThe structure of the cataract causing P23T mutant of human gamma-D crystallin
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / crystallin / cataract / protein / lens / Disease mutation / Eye lens protein / Oxidation / 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
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 / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsJung, J. / Byeon, I.L. / Wang, Y. / King, J. / Gronenborn, A.M.
CitationJournal: Biochemistry / Year: 2009
Title: The structure of the cataract-causing P23T mutant of human gammaD-crystallin exhibits distinctive local conformational and dynamic changes.
Authors: Jung, J. / Byeon, I.J. / Wang, Y. / King, J. / Gronenborn, A.M.
History
DepositionFeb 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 20, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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)21,8561
Polymers21,8561
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 21856.346 Da / Num. of mol.: 1 / Mutation: P23T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Rosetta 2 / Gene: CRYGD, CRYG4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P07320

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D HNCA
1313D CBCA(CO)NH
1413D (H)CCH-TOCSY
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1812D 1H-15N HSQC
1922D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-0.8 mM [U-99% 13C; U-99% 15N] p23t, 20 mM sodium phosphate, 5 mM DTT, 5 % [U-2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
20.2-0.8 mM [U-99% 13C; U-99% 15N] p23t, 20 mM sodium phosphate, 5 mM DTT, 5 % [U-2H] D2O, 5 % Pentaethylene glycol monododecyl ether, 5.2 % hexanol, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMp23t-1[U-99% 13C; U-99% 15N]0.2-0.81
20 mMsodium phosphate-21
5 mMDTT-31
5 %D2O-4[U-2H]1
mMp23t-5[U-99% 13C; U-99% 15N]0.2-0.82
20 mMsodium phosphate-62
5 mMDTT-72
5 %D2O-8[U-2H]2
5 %Pentaethylene glycol monododecyl ether-92
5.2 %hexanol-102
Sample conditionsIonic strength: 0.025333 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANABrunger A. T. et.al.geometry optimization
CYANABrunger A. T. et.al.structure solution
SparkyGoddardchemical shift assignment
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 4018 / NOE intraresidue total count: 734 / NOE long range total count: 1821 / NOE medium range total count: 471 / NOE sequential total count: 992 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 67 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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