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- PDB-7n3b: Crystal structure of aged 9-site deamidated variant of human gamm... -

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Basic information

Entry
Database: PDB / ID: 7n3b
TitleCrystal structure of aged 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: 2.09 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 6, 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
B: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)41,9372
Polymers41,9372
Non-polymers00
Water2,216123
1
A: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9691
Polymers20,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9691
Polymers20,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.650, 75.838, 93.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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


Mass: 20968.500 Da / Num. of mol.: 2 / 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.: 123 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 5.45, 0.1 M ammonium sulfate, 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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.09→58.87 Å / Num. obs: 20969 / % possible obs: 99.73 % / Redundancy: 12.9 % / Biso Wilson estimate: 39.04 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.98
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 2008 / CC1/2: 0.674

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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: 2.09→58.87 Å / SU ML: 0.2998 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 1083 5.17 %
Rwork0.1884 19879 -
obs0.191 20962 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.7 Å2
Refinement stepCycle: LAST / Resolution: 2.09→58.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 0 123 2997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733024
X-RAY DIFFRACTIONf_angle_d0.94264088
X-RAY DIFFRACTIONf_chiral_restr0.0635391
X-RAY DIFFRACTIONf_plane_restr0.0059540
X-RAY DIFFRACTIONf_dihedral_angle_d25.02331130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.190.35291280.2812395X-RAY DIFFRACTION98.52
2.19-2.30.31811350.25312463X-RAY DIFFRACTION99.92
2.3-2.450.34051350.25352452X-RAY DIFFRACTION99.92
2.45-2.640.2881440.23652430X-RAY DIFFRACTION99.92
2.64-2.90.34251440.22042463X-RAY DIFFRACTION99.92
2.9-3.320.24351310.19922498X-RAY DIFFRACTION100
3.32-4.190.22951410.15352512X-RAY DIFFRACTION99.85
4.19-58.870.15531250.15812666X-RAY DIFFRACTION99.86

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