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- PDB-8h0r: Crystal structure of a cataract-causing crystallin mutant (mouse ... -

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Basic information

Entry
Database: PDB / ID: 8h0r
TitleCrystal structure of a cataract-causing crystallin mutant (mouse CRYBB1 Y202X)
ComponentsBeta-crystallin B1B
KeywordsSTRUCTURAL PROTEIN / crystallin CRYBB1 / trancated mutant
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
Similarity search - Function
Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.201 Å
AuthorsJing, X. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82101102 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Cataract-causing Y204X mutation of crystallin protein CRY beta B1 promotes its C-terminal degradation and higher-order oligomerization.
Authors: Jing, X. / Zhu, M. / Lu, X. / Wei, P. / Shi, L. / Zhang, B.Y. / Xu, Y. / Tang, Y.P. / Xiang, D.M. / Gong, P.
History
DepositionSep 30, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-crystallin B1B
B: Beta-crystallin B1B


Theoretical massNumber of molelcules
Total (without water)21,5182
Polymers21,5182
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Polymer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.919, 48.437, 113.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-crystallin B1B


Mass: 10759.116 Da / Num. of mol.: 2 / Fragment: CRYBB1
Source method: isolated from a genetically manipulated source
Details: Protein degradated / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crybb1 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WVJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.55 Å3/Da / Density % sol: 51.68 % / Mosaicity: 0.44 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 6 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 68183 / % possible obs: 98.1 % / Redundancy: 10.4 % / Biso Wilson estimate: 14.36 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Χ2: 0.959 / Net I/σ(I): 17.5 / Num. measured all: 712380
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.244.60.48258070.8460.240.5430.82884.5
1.24-1.296.90.38566710.9340.1540.4160.87197.6
1.29-1.359.60.28768510.9790.0970.3030.925100
1.35-1.4211.90.20769000.990.0620.2161.003100
1.42-1.5112.40.1468610.9950.0410.1461.001100
1.51-1.6312.50.169020.9970.0290.1041.021100
1.63-1.7912.10.07569800.9980.0230.0790.986100
1.79-2.0511.60.0669310.9980.0180.0630.971100
2.05-2.5911.30.05470390.9980.0170.0570.88100
2.59-5010.50.0572410.9980.0160.0520.95598.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.201→23.103 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 3398 4.99 %
Rwork0.185 64698 -
obs0.1855 68096 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.37 Å2 / Biso mean: 19.4381 Å2 / Biso min: 10.1 Å2
Refinement stepCycle: final / Resolution: 1.201→23.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 0 187 1656
Biso mean---30 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061554
X-RAY DIFFRACTIONf_angle_d0.892105
X-RAY DIFFRACTIONf_chiral_restr0.093209
X-RAY DIFFRACTIONf_plane_restr0.005277
X-RAY DIFFRACTIONf_dihedral_angle_d12.159924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.201-1.21790.31771060.2664214779
1.2179-1.23610.26971140.2594235687
1.2361-1.25540.27111290.2398252093
1.2554-1.2760.26931430.2347266998
1.276-1.2980.2431480.2262266699
1.298-1.32160.21451330.21852719100
1.3216-1.3470.23371420.21542736100
1.347-1.37450.22621360.21242738100
1.3745-1.40440.24311460.20832679100
1.4044-1.4370.2351510.20342740100
1.437-1.4730.21421530.19252724100
1.473-1.51280.20771480.19432708100
1.5128-1.55730.19141450.19122744100
1.5573-1.60750.17881610.18952719100
1.6075-1.6650.20941380.18782750100
1.665-1.73160.17411470.1832743100
1.7316-1.81040.20391480.18062736100
1.8104-1.90580.21151620.18332754100
1.9058-2.02510.20191530.17372744100
2.0251-2.18140.18321180.17612779100
2.1814-2.40070.17121410.18222797100
2.4007-2.74760.20521410.19732806100
2.7476-3.45980.16741620.16742830100
3.4598-23.1030.18321330.1687289497

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