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- PDB-7n37: Crystal structure of 3-site deamidated variant of human gamma(S)-... -

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Basic information

Entry
Database: PDB / ID: 7n37
TitleCrystal structure of 3-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: 1.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1963
Polymers20,9631
Non-polymers2342
Water3,261181
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)29.449, 62.552, 79.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 20962.588 Da / Num. of mol.: 1 / Mutation: N15D,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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.75 Å3/Da / Density % sol: 29.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl2, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 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: 1.3→27.62 Å / Num. obs: 36161 / % possible obs: 97.57 % / Redundancy: 13.1 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 1 / Net I/σ(I): 27.64
Reflection shellResolution: 1.3→1.35 Å / Num. unique obs: 3477 / CC1/2: 0.795

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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: 1.3→27.62 Å / SU ML: 0.1313 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1793 1811 5.01 %
Rwork0.1451 34347 -
obs0.1469 36158 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.73 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 15 181 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01391601
X-RAY DIFFRACTIONf_angle_d1.30472175
X-RAY DIFFRACTIONf_chiral_restr0.1208207
X-RAY DIFFRACTIONf_plane_restr0.0097285
X-RAY DIFFRACTIONf_dihedral_angle_d26.603643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.34461300.24552523X-RAY DIFFRACTION94.28
1.34-1.370.27821190.20862566X-RAY DIFFRACTION96.62
1.37-1.420.24191300.17962580X-RAY DIFFRACTION96.44
1.42-1.470.2341440.16182573X-RAY DIFFRACTION96.21
1.47-1.530.21921540.14712615X-RAY DIFFRACTION98.37
1.53-1.60.20061410.12792610X-RAY DIFFRACTION97.87
1.6-1.680.181260.12042623X-RAY DIFFRACTION97.72
1.68-1.790.20331220.12722617X-RAY DIFFRACTION96.48
1.79-1.930.17461400.12582649X-RAY DIFFRACTION98.14
1.93-2.120.16881540.12812675X-RAY DIFFRACTION98.54
2.12-2.430.18831370.13932727X-RAY DIFFRACTION99.62
2.43-3.050.20941540.15942735X-RAY DIFFRACTION99.55
3.06-27.620.14371600.14392854X-RAY DIFFRACTION98.37

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