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- PDB-1e7n: The N-terminal domain of beta-B2-crystallin resembles the putativ... -

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Basic information

Entry
Database: PDB / ID: 1e7n
TitleThe N-terminal domain of beta-B2-crystallin resembles the putative ancestral homodimer
ComponentsBETA-CRYSTALLIN B2
KeywordsSTRUCTURAL PROTEIN / EYE LENS PROTEIN / DOMAIN INTERACTIONS / 2-FOLD SYMMETRY
Function / homology
Function and homology information


structural constituent of eye lens / camera-type eye development / lens development in camera-type eye / visual perception / identical protein binding
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 speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsClout, N.J. / Basak, A. / Wieligmann, K. / Bateman, O.A. / Jaenicke, R. / Slingsby, C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The N-Terminal Domain of Betab2-Crystallin Resembles the Putative Ancestral Homodimer.
Authors: Clout, N.J. / Basak, A. / Wieligmann, K. / Bateman, O.A. / Jaenicke, R. / Slingsby, C.
History
DepositionAug 31, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Category: diffrn_detector
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-CRYSTALLIN B2
B: BETA-CRYSTALLIN B2


Theoretical massNumber of molelcules
Total (without water)23,8222
Polymers23,8222
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-1.9 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.960, 110.960, 29.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.178, 0.984, -0.004), (0.984, 0.178, 0.013), (0.013, -0.001, -1)
Vector: -0.49859, -0.23629, 46.97172)

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Components

#1: Protein BETA-CRYSTALLIN B2 / BETA-B2 CRYSTALLIN / BETA-CRYSTALLIN BP


Mass: 11911.123 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 2-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62696
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDOMINANT COMPONENT OF EYE LENS IN VERTEBRATE
Sequence detailsONLY N-TERMINAL DOMAIN PRESENT.

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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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
20.2 Mmagnesium acetate tetrahydrate1reservoir
30.1 Msodium cacodylate1reservoir
415 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 9079 / % possible obs: 99.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.057
Reflection
*PLUS
Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
CNS0.9refinement
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.89 Å / Rfactor Rfree error: 0.012 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE N-TERMINAL 13 RESIDUE EXTENSION WAS NOT SEEN IN THE DENSITY C-TERMINAL LAST FOUR RESIDUES WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 446 4.9 %RANDOM
Rwork0.212 ---
obs0.212 9056 99.8 %-
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å23.87 Å20 Å2
2---0.41 Å20 Å2
3---0.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 0 61 1464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 73 4.9 %
Rwork0.262 1425 -
obs--99.5 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.2049
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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