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- PDB-5vh1: Crystal Structure of Chicken Gamma S Crystallin -

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Basic information

Entry
Database: PDB / ID: 5vh1
TitleCrystal Structure of Chicken Gamma S Crystallin
ComponentsGamma S-crystallin
KeywordsPROTEIN BINDING / crystallin lens beta sheet two domain
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSagar, V. / Wistow, G.
CitationJournal: Structure / Year: 2017
Title: Crystal Structure of Chicken gamma S-Crystallin Reveals Lattice Contacts with Implications for Function in the Lens and the Evolution of the beta gamma-Crystallins.
Authors: Sagar, V. / Chaturvedi, S.K. / Schuck, P. / Wistow, G.
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 5V14
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma S-crystallin


Theoretical massNumber of molelcules
Total (without water)20,6961
Polymers20,6961
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.910, 41.010, 49.460
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-353-

HOH

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Components

#1: Protein Gamma S-crystallin


Mass: 20696.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CRYGS / Production host: Escherichia coli (E. coli) / References: UniProt: D0UYB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium acetate pH 7.1 and 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 7149 / % possible obs: 95 % / Redundancy: 3.3 % / Rsym value: 0.053 / Net I/σ(I): 40

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZWO

1zwo


Resolution: 2.3→26.241 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 357 4.99 %
Rwork0.1319 --
obs0.1355 7149 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→26.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 0 155 1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081521
X-RAY DIFFRACTIONf_angle_d0.9212062
X-RAY DIFFRACTIONf_dihedral_angle_d23.055893
X-RAY DIFFRACTIONf_chiral_restr0.057195
X-RAY DIFFRACTIONf_plane_restr0.006277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.63260.27281040.16052195X-RAY DIFFRACTION97
2.6326-3.31570.24181150.14212284X-RAY DIFFRACTION100
3.3157-26.24280.16111380.11552313X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -5.6334 Å / Origin y: -20.8446 Å / Origin z: 12.2005 Å
111213212223313233
T0.0407 Å20.0154 Å2-0.0066 Å2-0.0296 Å2-0.0055 Å2--0.0336 Å2
L0.4985 °2-0.0672 °2-0.2132 °2-0.0773 °20.0701 °2--0.2541 °2
S0.0538 Å °0.0899 Å °-0.056 Å °0.0038 Å °0.0042 Å °0.0125 Å °0.0004 Å °0.0124 Å °0.0672 Å °
Refinement TLS groupSelection details: chain 'A' and ((resseq 1:177))

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