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- PDB-1a45: GAMMAF CRYSTALLIN FROM BOVINE LENS -

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Basic information

Entry
Database: PDB / ID: 1a45
TitleGAMMAF CRYSTALLIN FROM BOVINE LENS
ComponentsGAMMAF 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNorledge, B.V. / Hay, R. / Bateman, O.A. / Slingsby, C. / White, H.E. / Moss, D.S. / Lindley, P.F. / Driessen, H.P.C.
Citation
Journal: Exp.Eye Res. / Year: 1997
Title: Towards a molecular understanding of phase separation in the lens: a comparison of the X-ray structures of two high Tc gamma-crystallins, gammaE and gammaF, with two low Tc gamma-crystallins, gammaB and gammaD.
Authors: Norledge, B.V. / Hay, R.E. / Bateman, O.A. / Slingsby, C. / Driessen, H.P.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Packing Interactions in the Eye-Lens. Structural Analysis, Internal Symmetry and Lattice Interactions of Bovine Gamma Iva-Crystallin
Authors: White, H.E. / Driessen, H.P. / Slingsby, C. / Moss, D.S. / Lindley, P.F.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: The Use of Pseudosymmetry in the Rotation Function of Gamma Iva-Crystallin
Authors: White, H.E. / Driessen, H.P. / Slingsby, C. / Moss, D.S. / Turnell, W.G. / Lindley, P.F.
#3: Journal: Exp.Eye Res. / Year: 1983
Title: Purification and Crystallization of Mammalian Lens Gamma-Crystallins
Authors: Slingsby, C. / Miller, L.R.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1978
Title: The Low-Resolution Structure Analysis of the Lens Protein Gamma-Crystallin
Authors: Blundell, T.L. / Lindley, P.F. / Moss, D.S. / Slingsby, C. / Tickle, I.J. / Turnell, W.G.
History
DepositionFeb 10, 1998Processing site: BNL
SupersessionJun 17, 1998ID: 2GCR
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMAF CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)20,9851
Polymers20,9851
Non-polymers00
Water3,729207
1
A: GAMMAF CRYSTALLIN

A: GAMMAF CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)41,9712
Polymers41,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)35.100, 46.200, 186.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GAMMAF CRYSTALLIN


Mass: 20985.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: LENS / References: UniProt: P23005
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES HAVE BEEN NUMBERED ACCORDING TO THE HOMOLOGY WITH BOVINE LENS GAMMA B-CRYSTALLIN. ...THE RESIDUES HAVE BEEN NUMBERED ACCORDING TO THE HOMOLOGY WITH BOVINE LENS GAMMA B-CRYSTALLIN. THEREFORE, THERE IS A GAP AT RESIDUE 85 (NORLEDGE ET AL., 1997).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 32 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD ON AN ARNDT-WONACOTT CAMERA. THERE IS INCOMPLETE DATA TO 2.1 A.
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
pH: 6.86 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 %(w/v)PEG60001drop
20.05 Msodium phosphate1drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.5418
DetectorDetector: FILM / Date: Jun 1, 1983
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→24 Å / Num. obs: 6300 / % possible obs: 88.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.104

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HANEEFrefinement
HARRISrefinement
HOWLINrefinement
KHANrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GCR

4gcr


Resolution: 2.3→8 Å / σ(F): 0
Details: THE AUTHORS ALSO USED REFINEMENT PROGRAM RESTRAIN (DRIESSEN, HANEEF, HARRIS, HOWLIN, KHAN & MOSS, J. APPL. CRYSTALLOGR. 22, 510, 1989).
RfactorNum. reflection% reflection
Rwork0.186 --
obs0.186 6115 88.6 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 0 207 1688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.623
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.478
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.478

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