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- PDB-2bb2: X-RAY ANALYSIS OF BETA B2-CRYSTALLIN AND EVOLUTION OF OLIGOMERIC ... -

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Basic information

Entry
Database: PDB / ID: 2bb2
TitleX-RAY ANALYSIS OF BETA B2-CRYSTALLIN AND EVOLUTION OF OLIGOMERIC LENS PROTEINS
ComponentsBETA B2-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
BETA-MERCAPTOETHANOL / Beta-crystallin B2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBax, B. / Lapatto, R. / Nalini, V. / Driessen, H. / Lindley, P.F. / Mahadevan, D. / Blundell, T.L. / Slingsby, C.
Citation
Journal: Nature / Year: 1990
Title: X-ray analysis of beta B2-crystallin and evolution of oligomeric lens proteins.
Authors: Bax, B. / Lapatto, R. / Nalini, V. / Driessen, H. / Lindley, P.F. / Mahadevan, D. / Blundell, T.L. / Slingsby, C.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization of a New Form of the Eye Lens Protein Beta B2-Crystallin
Authors: Bax, B. / Slingsby, C.
History
DepositionSep 21, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA B2-CRYSTALLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8973
Polymers20,7411
Non-polymers1562
Water1,65792
1
A: BETA B2-CRYSTALLIN
hetero molecules

A: BETA B2-CRYSTALLIN
hetero molecules

A: BETA B2-CRYSTALLIN
hetero molecules

A: BETA B2-CRYSTALLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,58912
Polymers82,9644
Non-polymers6258
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
2
A: BETA B2-CRYSTALLIN
hetero molecules

A: BETA B2-CRYSTALLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7956
Polymers41,4822
Non-polymers3134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area4760 Å2
ΔGint-19 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.800, 83.600, 109.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: SG SEO 22 IS BONDED TO SG CYS 22. / 2: RESIDUE 41 IS A CIS PROLINE. / 3: SG SEO 50 IS BONDED TO SG CYS 50.

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Components

#1: Protein BETA B2-CRYSTALLIN


Mass: 20741.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P02522
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein 1drop
20.05 MTris-acetate1drop
31 mMdithiothreitol1drop
40.02 %(w/v)sodium azide1drop
535 %(v/v)methanepentanediol1reservoir
618 mMcalcium acetate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 18000 / Rmerge(I) obs: 0.063

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.186 / Rfactor obs: 0.186 / Highest resolution: 2.1 Å
Details: THE ELECTRON DENSITY MAPS IN THE REGION OF RESIDUES CYS 22 AND CYS 50 (AT THE 3 SIGMA LEVEL) OF THE HIGHLY REFINED STRUCTURE OF BETA-B2 AT 2.1 A (I222 CRYSTAL FORM), SHOW ADDITIONAL DENSITY ...Details: THE ELECTRON DENSITY MAPS IN THE REGION OF RESIDUES CYS 22 AND CYS 50 (AT THE 3 SIGMA LEVEL) OF THE HIGHLY REFINED STRUCTURE OF BETA-B2 AT 2.1 A (I222 CRYSTAL FORM), SHOW ADDITIONAL DENSITY WHICH IS INTERPRETED AS A MIXED DISULFIDE WITH BETA-MERCAPTOETHANOL OR DITHIOTHREITOL. AS BETA-MERCAPTOETHANOL FRAGMENT IS COMMON TO BOTH, A DISULFIDE BRIDGE WITH BETA-MERCAPTOETHANOL WAS MODELLED AT RESIDUES 22 AND 50 AND REFINED INTO DENSITY WITH A S-S DISTANCE OF 2.08 A. ELECTRON DENSITY FOR THE CYS 22 ADDUCT INDICATED TWO POSITIONS. THE MAJOR SITE (55% OCCUPANCY) IS A RIGHT HANDED DISULFIDE, WITH CHI 3 = 85, THE MINOR SITE (45% OCCUPANCY), IS A LEFT HANDED SPIRAL DISULFIDE, CHI 3 = -79. A RIGHT HANDED DISULFIDE, CHI 3 = 87 WAS BUILT INTO THE ELECTRON DENSITY AT CYS 50. THESE MODELS WERE SUBSEQUENTLY REFINED USING RESTRAIN. THE RESULTING CONFORMATIONS OF THE MIXED DISULFIDES WERE CONFIRMED BY CALCULATING OMIT ELECTRON DENSITY MAPS.
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 8 92 1564
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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