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- PDB-7n3a: Crystal structure of 9-site deamidated variant of human gamma(S)-... -

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Basic information

Entry
Database: PDB / ID: 7n3a
TitleCrystal structure of 9-site deamidated variant of 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: 1.5 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9691
Polymers20,9691
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.770, 57.710, 44.950
Angle α, β, γ (deg.)90.000, 103.330, 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: 20968.500 Da / Num. of mol.: 1 / Mutation: N15D,Q17E,N54D,Q64E,Q71E,Q93E,Q107E,Q121E,N144D
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.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.79 Å3/Da / Density % sol: 31.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate pH 5.45, 21% PEG 3350

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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: 1.5→43.74 Å / Num. obs: 23517 / % possible obs: 98.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.38 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.85
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 2292 / CC1/2: 0.734

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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: 1.5→43.74 Å / SU ML: 0.2225 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.7047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2237 1147 4.91 %
Rwork0.1953 22231 -
obs0.1968 23378 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 110 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781517
X-RAY DIFFRACTIONf_angle_d0.98742058
X-RAY DIFFRACTIONf_chiral_restr0.0702198
X-RAY DIFFRACTIONf_plane_restr0.0072271
X-RAY DIFFRACTIONf_dihedral_angle_d23.8274565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.570.48571360.45082728X-RAY DIFFRACTION96.92
1.57-1.650.46051430.38192749X-RAY DIFFRACTION97.7
1.65-1.750.33731210.322776X-RAY DIFFRACTION98.17
1.75-1.890.31181330.26772780X-RAY DIFFRACTION99.12
1.89-2.080.27941520.2232782X-RAY DIFFRACTION98.85
2.08-2.380.22951680.20542747X-RAY DIFFRACTION98.05
2.38-30.2391520.2042817X-RAY DIFFRACTION99.26
3-43.740.1641420.14712852X-RAY DIFFRACTION99.17

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