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- PDB-7n39: Crystal structure of 7-site deamidated variant of human gamma(S)-... -

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Basic information

Entry
Database: PDB / ID: 7n39
TitleCrystal structure of 7-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: 1.56 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0293
Polymers41,9332
Non-polymers961
Water5,531307
1
A: Gamma-crystallin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0632
Polymers20,9671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)20,9671
Polymers20,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.146, 76.629, 94.655
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: 20966.529 Da / Num. of mol.: 2 / Mutation: N15D,Q17E,N54D,Q64E,Q93E,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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 5.0, 0.1 M ammonium sulfate, 28% 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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.56→40.27 Å / Num. obs: 51461 / % possible obs: 99.61 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.19 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.17
Reflection shellResolution: 1.56→1.62 Å / Num. unique obs: 5051 / CC1/2: 0.927

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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: 1.56→40.27 Å / SU ML: 0.1828 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 2650 5.15 %
Rwork0.1934 48797 -
obs0.1944 51447 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.75 Å2
Refinement stepCycle: LAST / Resolution: 1.56→40.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 5 307 3180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633246
X-RAY DIFFRACTIONf_angle_d0.81314415
X-RAY DIFFRACTIONf_chiral_restr0.0592417
X-RAY DIFFRACTIONf_plane_restr0.0061594
X-RAY DIFFRACTIONf_dihedral_angle_d26.95721245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.590.331280.3112521X-RAY DIFFRACTION98.51
1.59-1.620.33871430.29522513X-RAY DIFFRACTION99.55
1.62-1.650.30161330.26742525X-RAY DIFFRACTION99.33
1.65-1.690.32231380.25172559X-RAY DIFFRACTION99.67
1.69-1.730.26371360.24162517X-RAY DIFFRACTION99.66
1.73-1.770.28441430.22832543X-RAY DIFFRACTION99.7
1.77-1.820.27161270.23482566X-RAY DIFFRACTION99.56
1.82-1.870.23591350.23552528X-RAY DIFFRACTION99.74
1.87-1.930.28931280.2292558X-RAY DIFFRACTION99.52
1.93-20.28151450.21682527X-RAY DIFFRACTION99.63
2-2.080.28571410.2232553X-RAY DIFFRACTION99.63
2.08-2.180.23591250.2112581X-RAY DIFFRACTION99.82
2.18-2.290.25791220.20662559X-RAY DIFFRACTION99.93
2.29-2.430.22931470.20832598X-RAY DIFFRACTION99.89
2.44-2.620.22591460.21152571X-RAY DIFFRACTION99.85
2.62-2.890.23551400.20992602X-RAY DIFFRACTION99.93
2.89-3.30.21391530.18952602X-RAY DIFFRACTION99.96
3.3-4.160.14711560.15512630X-RAY DIFFRACTION99.79
4.16-40.270.18331640.16532744X-RAY DIFFRACTION99.32

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