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- PDB-1elp: GAMMA-D CRYSTALLIN STRUCTURE AT 1.95 A RESOLUTION -

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Entry
Database: PDB / ID: 1elp
TitleGAMMA-D CRYSTALLIN STRUCTURE AT 1.95 A RESOLUTION
ComponentsGAMMA-D CRYSTALLIN
KeywordsEYE LENS PROTEIN
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsChirgadze, Yu.N. / Driessen, H.P.C. / Wright, G. / Slingsby, C. / Hay, R.E. / Lindley, P.F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of bovine eye lens gammaD (gammaIIIb)-crystallin at 1.95 A.
Authors: Chirgadze, Y.N. / Driessen, H.P. / Wright, G. / Slingsby, C. / Hay, R.E. / Lindley, P.F.
#1: Journal: Exp.Eye Res. / Year: 1991
Title: Crystal Structure of Calf Eye Lens Gamma-Crystallin Iiib at 2.5 A Resolution: Its Relation to Function
Authors: Chirgadze, Yu. / Nevskaya, N. / Vernoslova, E. / Nikonov, S. / Sergeev, Yu. / Brazhnikov, E. / Fomenkova, N. / Lunin, V. / Urzhumtsev, A.
#2: Journal: Proteins / Year: 1988
Title: Surface Interactions of Gamma-Crystallins in the Crystal Medium in Relation to Their Association in the Eye Lens
Authors: Sergeev, Y.V. / Chirgadze, Y.N. / Mylvaganam, S.E. / Driessen, H. / Slingsby, C. / Blundell, T.L.
#3: Journal: Mol.Biol.(Moscow) / Year: 1987
Title: [the Key Role of the Residue 103 in the Surface Interactions of Gamma-Crystallins]
Authors: Sergeev, Iu.V. / Chirgadze, Iu.N. / Driessen, H. / Slingsby, C. / Blundell, T.L.
#4: Journal: Mol.Biol.(Engl.Transl.) / Year: 1987
Title: Key Role of Residue 103 in Surface Interactions of Gamma-Crystallins
Authors: Sergeev, Yu.V. / Chirgadze, Yu.N. / Driessen, H. / Slingsby, C. / Blundell, T.L.
#5: Journal: Dokl.Akad.Nauk Sssr / Year: 1986
Title: Spatial Structure of Gamma-Crystallin Iiib from Calf Eye Lens at 2.5 Angstroms Resolution
Authors: Chirgadze, Yu.N. / Nevskaya, N.A. / Fomenkova, N.P. / Nikonov, S.V. / Sergeev, Yu.V. / Brazhnikov, E.V. / Garber, M.B. / Lunin, V.Yu. / Urzumtsev, A.P. / Vernoslova, E.A.
#6: Journal: Acta Crystallogr.,Sect.A / Year: 1985
Title: Phase Improvement in Protein Crystallography Using a Mixed Electron Density Model
Authors: Lunin, V.Yu. / Urzhumtsev, A.G. / Vernoslova, E.A. / Chirgadze, Yu.N. / Nevskaya, N.A. / Fomenkova, N.P.
#7: Journal: Acta Crystallogr.,Sect.A / Year: 1984
Title: Improvement of Protein Phases by Coarse Model Modification
Authors: Lunin, V.Yu. / Urzhumtsev, A.G.
#8: Journal: Dokl.Akad.Nauk Sssr / Year: 1981
Title: Structure of Gamma-Crystallin Iiib from the Eye Lens of the Calf at 3 Angstroms Resolution
Authors: Chirgadze, Yu.N. / Sergeev, Yu.V. / Fomenkova, N.P. / Oreshin, V.D. / Nikonov, S.V.
#9: Journal: FEBS Lett. / Year: 1981
Title: Polypeptide Chain Pathway in Gamma-Crystallin Iiib from Calf Lens at 3 A Resolution
Authors: Chirgadze, Yu.N. / Sergeev, Yu.V. / Fomenkova, N.P. / Oreshin, V.D.
#10: Journal: FEBS Lett. / Year: 1980
Title: Structure of Gamma-Crystallin Iiib from Calf Lens at 5 A Resolution
Authors: Chirgadze, Y.N. / Oreshin, V.D. / Sergeev, Y.V. / Nikonov, S.V. / Lunin, V.Y.
#11: Journal: J.Mol.Biol. / Year: 1977
Title: Crystallographic Study of Gamma-Crystallins from Calf Lens
Authors: Chirgadze, Y.N. / Nikonov, S.V. / Garber, M.B. / Reshetnikova, L.S.
#12: Journal: Dokl.Akad.Nauk Sssr / Year: 1976
Title: Growing Single Crystals of Gamma Crystallin from the Calf Crystalline Lens
Authors: Garber, M.B. / Reshetnikova, L.S.
History
DepositionDec 20, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMA-D CRYSTALLIN
B: GAMMA-D CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)41,5562
Polymers41,5562
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.810, 70.030, 117.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GAMMA-D CRYSTALLIN


Mass: 20778.236 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: EYE / Tissue: EYE LENS / References: UniProt: P08209
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein11
21 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 33667 / % possible obs: 95.2 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.081
Reflection
*PLUS
Highest resolution: 1.95 Å / Num. measured all: 144932

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Processing

Software
NameClassification
RESTRAINrefinement
DENZOdata reduction
RefinementResolution: 1.95→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.204 --
obs-33104 95.2 %
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 0 219 3147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.924
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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