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- PDB-1a5d: GAMMAE CRYSTALLIN FROM RAT LENS -

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Basic information

Entry
Database: PDB / ID: 1a5d
TitleGAMMAE CRYSTALLIN FROM RAT LENS
ComponentsGAMMAE 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNorledge, B.V. / Hay, R. / Bateman, O.A. / Slingsby, C. / Driessen, H.P.C.
CitationJournal: 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.
History
DepositionFeb 12, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 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: GAMMAE CRYSTALLIN
B: GAMMAE CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)42,3272
Polymers42,3272
Non-polymers00
Water4,630257
1
A: GAMMAE CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)21,1641
Polymers21,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GAMMAE CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)21,1641
Polymers21,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.760, 43.710, 107.440
Angle α, β, γ (deg.)90.00, 108.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9997, 0.0217, -0.0055), (0.0216, -0.9997, -0.0132), (-0.0058, 0.0131, -0.9999)
Vector: -20.354, 25.392, 51.078)
DetailsTHE MOST LIKELY ACTIVE BIOLOGICAL STATE IS MONOMERIC.

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Components

#1: Protein GAMMAE CRYSTALLIN


Mass: 21163.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LENS / References: UniProt: P02528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.05 %
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-IDDetails
20.05 Msodium phosphate1drop
30.02 %sodium azide1drop
43 mMdithiothreitol1drop
513 %(w/v)PEG60001reservoir
60.05 Msodium phosphate1reservoir
1protein1drop6.2mg

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceType: BRUKER NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 1, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50.9 Å / Num. obs: 12942 / % possible obs: 84.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Num. measured all: 41615

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HANEEFrefinement
HARRISrefinement
HOWLINrefinement
KHANrefinement
MADNESdata reduction
PRECURSORTO ABSURD/ ROTAVATA/AGROVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GCR

2gcr
PDB Unreleased entry


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). THERE WAS NO ELECTRON DENSITY FOR THE SIDE CHAINS OF ...Details: THE AUTHORS ALSO USED REFINEMENT PROGRAM RESTRAIN (DRIESSEN, HANEEF, HARRIS, HOWLIN, KHAN & MOSS, J. APPL. CRYSTALLOGR. 22, 510, 1989). THERE WAS NO ELECTRON DENSITY FOR THE SIDE CHAINS OF SER B 58 AND SER B 119.
RfactorNum. reflection% reflection
Rwork0.168 --
obs0.168 12564 85.7 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 0 257 3230
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_deg1.696
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.05
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.514
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_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.91
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.053
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.514

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