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- PDB-1amm: 1.2 ANGSTROM STRUCTURE OF GAMMA-B CRYSTALLIN AT 150K -

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Basic information

Entry
Database: PDB / ID: 1amm
Title1.2 ANGSTROM STRUCTURE OF GAMMA-B CRYSTALLIN AT 150K
ComponentsGAMMA B-CRYSTALLIN
KeywordsCRYSTALLIN / EYE 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 / Beta/Gamma crystallin / Gamma-B Crystallin; domain 1 / 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 / SYNCHROTRON / Resolution: 1.2 Å
AuthorsKumaraswamy, V.S. / Lindley, P.F. / Slingsby, C. / Glover, I.D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: An eye lens protein-water structure: 1.2 A resolution structure of gammaB-crystallin at 150 K.
Authors: Kumaraswamy, V.S. / Lindley, P.F. / Slingsby, C. / Glover, I.D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of the Bovine Eye Lens Protein Gamma B (Gamma II) Crystallin at 1.47 Angstroms
Authors: Najmudin, S. / Nalini, V. / Driessen, H.P.C. / Slingsby, C. / Blundell, T.L. / Moss, D.S. / Lindley, P.F.
#2: Journal: J.Chem.Soc.,Faraday Trans. / Year: 1993
Title: Structure of Gammab-Crystallin at 150K
Authors: Lindley, P.F. / Najmudin, S. / Bateman, O. / Slingsby, C. / Myles, D.D. / Kumaraswamy, S. / Glover, I.
History
DepositionMar 20, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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
Water7,062392
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.430, 56.430, 97.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

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Components

#1: Protein GAMMA B-CRYSTALLIN / GAMMA II-CRYSTALLIN


Mass: 20992.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: EYE / Tissue: EYE LENSLens (anatomy) / References: UniProt: P02526
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 1.84 Å3/Da / Density % sol: 35 %
Crystal grow
*PLUS
Temperature: 0 K / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein11
20.05 Msodium hydrogen phosphate11
31 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.98
DetectorType: CEA FILM / Detector: FILM / Date: Aug 1, 1992 / Details: FOCUSSING MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.18→20 Å / Num. obs: 45977 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 3.76 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.8
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.3 / % possible all: 88
Reflection
*PLUS
Num. measured all: 173126
Reflection shell
*PLUS
% possible obs: 88 % / Num. unique obs: 5317 / Num. measured obs: 16578

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Processing

Software
NameClassification
RESTRAINrefinement
MOSFLMdata reduction
RefinementResolution: 1.2→12 Å / σ(F): 0 /
Num. reflection% reflection
all45905 -
obs45905 93.8 %
Displacement parametersBiso mean: 8.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 0 392 1878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.054
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.032
X-RAY DIFFRACTIONp_chiral_restr0.023
X-RAY DIFFRACTIONp_singtor_nbd0.035
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Num. reflection all: 49721 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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