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- PDB-7n36: Crystal structure of wild-type human gamma(S)-crystallin -

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Basic information

Entry
Database: PDB / ID: 7n36
TitleCrystal structure of wild-type human gamma(S)-crystallin
ComponentsGamma-crystallin S
KeywordsSTRUCTURAL PROTEIN / crystallin / human crystallin / gamma(S) crystallin / eye lens protein
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
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNorton-Baker, B. / Mehrabi, P. / Martin, R.W.
CitationJournal: Structure / Year: 2022
Title: Deamidation of the human eye lens protein gamma S-crystallin accelerates oxidative aging.
Authors: Norton-Baker, B. / Mehrabi, P. / Kwok, A.O. / Roskamp, K.W. / Rocha, M.A. / Sprague-Piercy, M.A. / von Stetten, D. / Miller, R.J.D. / Martin, R.W.
History
DepositionMay 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-crystallin S
B: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)41,9192
Polymers41,9192
Non-polymers00
Water2,126118
1
A: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.840, 60.630, 56.030
Angle α, β, γ (deg.)90.000, 117.462, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Gamma-crystallin S / Beta-crystallin S / Gamma-S-crystallin


Mass: 20959.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, CRYG8 / Production host: Escherichia coli (E. coli) / References: UniProt: P22914
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Morpheus condition G5 (0.1 M Carboxylic Acids Mix, 0.1 M Buffer System 2 pH 7.5, 30 % v/v Precipitant Mix 1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→46.89 Å / Num. obs: 20807 / % possible obs: 97.42 % / Redundancy: 7 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.29
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 2056 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FD8

6fd8


Resolution: 2→46.89 Å / SU ML: 0.2381 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2199 962 4.63 %
Rwork0.1891 19835 -
obs0.1907 20797 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.59 Å2
Refinement stepCycle: LAST / Resolution: 2→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 0 118 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553001
X-RAY DIFFRACTIONf_angle_d0.87754058
X-RAY DIFFRACTIONf_chiral_restr0.0621389
X-RAY DIFFRACTIONf_plane_restr0.0049535
X-RAY DIFFRACTIONf_dihedral_angle_d22.04331116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.31631510.24282772X-RAY DIFFRACTION97.01
2.11-2.240.28311340.22772844X-RAY DIFFRACTION97.51
2.24-2.410.28471420.22112768X-RAY DIFFRACTION96.81
2.41-2.650.29331080.21682885X-RAY DIFFRACTION97.78
2.65-3.040.27711270.21422837X-RAY DIFFRACTION98.05
3.04-3.830.19021620.18662835X-RAY DIFFRACTION97.5
3.83-46.890.18721380.16222894X-RAY DIFFRACTION97.34

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