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- PDB-1gam: GAMMA B CRYSTALLIN TRUNCATED C-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1gam
TitleGAMMA B CRYSTALLIN TRUNCATED C-TERMINAL DOMAIN
ComponentsGAMMA B CRYSTALLIN
KeywordsEYE-LENS PROTEIN / GAMMA CRYSTALLIN B / EYE LENS PROTEIN / MULTIGENE FAMILY
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 / Resolution: 2.6 Å
AuthorsNorledge, B.V. / Mayr, E.-M. / Glockshuber, R. / Bateman, O.A. / Slingsby, C. / Jaenicke, R. / Driessen, H.P.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: The X-ray structures of two mutant crystallin domains shed light on the evolution of multi-domain proteins.
Authors: Norledge, B.V. / Mayr, E.M. / Glockshuber, R. / Bateman, O.A. / Slingsby, C. / Jaenicke, R. / Driessen, H.P.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Domain Interactions and Connecting Peptides in Lens Crystallins
Authors: Mayr, E.M. / Jaenicke, R. / Glockshuber, R.
History
DepositionFeb 2, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 B CRYSTALLIN
B: GAMMA B CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)20,7062
Polymers20,7062
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.480, 36.480, 232.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GAMMA B CRYSTALLIN


Mass: 10352.777 Da / Num. of mol.: 2 / Fragment: TRUNCATED C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle)
Description: EXPRESSION SYSTEM FOR ENGINEERED MUTANT FOLLOWED BY REMOVAL OF C-TERMINAL TYROSINE RESIDUE BY PROTEOLYSIS
Organ: EYE / Production host: Escherichia coli (E. coli) / References: UniProt: P02526
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GAMMA B CRYSTALLIN TRUNCATED C-TERMINAL DOMAIN CONSISTS OF RESIDUES 87 - 173 OF THE COMPLETE ...THE GAMMA B CRYSTALLIN TRUNCATED C-TERMINAL DOMAIN CONSISTS OF RESIDUES 87 - 173 OF THE COMPLETE GAMMA B CRYSTALLIN. THE NUMBERING FOLLOWS THAT OF THE COMPLETE PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.35 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.8 mg/mlgammaB-C1drop
20.1 M1dropNaCl-HCl
30.2 M1reservoir(NH4)2SO4
430 %(w/v)PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 9345 / Rmerge(I) obs: 0.07
Reflection
*PLUS
% possible obs: 95.5 % / Num. measured all: 43347

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å /
RfactorNum. reflection
Rwork0.21 -
obs0.21 9306
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms478 0 0 37 515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.02
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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