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- PDB-4gcr: STRUCTURE OF THE BOVINE EYE LENS PROTEIN GAMMA-B (GAMMA-II)-CRYST... -

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Basic information

Entry
Database: PDB / ID: 4gcr
TitleSTRUCTURE OF THE BOVINE EYE LENS PROTEIN GAMMA-B (GAMMA-II)-CRYSTALLIN AT 1.47 ANGSTROMS
ComponentsGAMMA-B 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 (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.47 Å
AuthorsSlingsby, C. / Najmudin, S. / Nalini, V. / Driessen, H.P.C. / Blundell, T.L. / Moss, D.S. / Lindley, P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of the bovine eye lens protein gammaB(gammaII)-crystallin at 1.47 A.
Authors: Najmudin, S. / Nalini, V. / Driessen, H.P. / Slingsby, C. / Blundell, T.L. / Moss, D.S. / Lindley, P.F.
#1: Journal: Pept.Protein Rev. / Year: 1984
Title: X-Ray Studies of the Lens Specific Proteins, the Crystallins
Authors: Summers, L. / Wistow, G. / Narebor, M. / Moss, D. / Lindley, P. / Slingsby, C. / Blundell, T. / Bartunik, H. / Bartels, K.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Gamma-II Crystallin at 1.9 Angstrom Resolution
Authors: Wistow, G. / Turnell, B. / Summers, L. / Slingsby, C. / Moss, D. / Miller, L. / Lindley, P. / Blundell, T.
#3: Journal: Nature / Year: 1981
Title: X-Ray Analysis of Gamma Crystallin II
Authors: Blundell, T. / Lindley, P. / Miller, L. / Moss, D. / Slingsby, C. / Tickle, I. / Turnell, B. / Wistow, G.
History
DepositionApr 2, 1992Processing site: BNL
SupersessionOct 15, 1993ID: 1GCR
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMA-B CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)20,9931
Polymers20,9931
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.530, 57.530, 97.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GAMMA-B CRYSTALLIN


Mass: 20992.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P02526
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A BETA-BRIDGE BETWEEN RESIDUES 119 - 121 AND 162 - 164.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal grow
*PLUS
Temperature: 0 K / pH: 7 / Method: unknown / Details: Carlisle, C.H.,(1977) J. Mol. Biol., 110, 417.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein11
20.05 Mphosphate12
31 mMdithiothreitol12

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Data collection

Reflection
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 9999 Å / Num. obs: 26151 / Rmerge(I) obs: 0.084 / Num. measured all: 118540

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.181 / Highest resolution: 1.47 Å
Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR COLUMN OF THE ATOM AND HETATM RECORDS BELOW IS UISO (U**2), WHICH IS THE MEAN-SQUARE AMPLITUDE VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR COLUMN OF THE ATOM AND HETATM RECORDS BELOW IS UISO (U**2), WHICH IS THE MEAN-SQUARE AMPLITUDE VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE RELATION: B = 8*(PI)**2*U**2.
Refinement stepCycle: LAST / Highest resolution: 1.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 0 230 1786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.038
Refinement
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 8 Å / Rfactor obs: 0.181 / Num. reflection obs: 29773
Solvent computation
*PLUS
Displacement parameters
*PLUS

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