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- PDB-9z75: Crystal Structure of Wild-type Mouse Gamma(S)-Crystallin -

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Basic information

Entry
Database: PDB / ID: 9z75
TitleCrystal Structure of Wild-type Mouse Gamma(S)-Crystallin
ComponentsGamma-crystallin S
KeywordsSTRUCTURAL PROTEIN / crystallin / lens
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.83 Å
AuthorsKeyes, A. / De-la-Torre, P. / Paschalis, E. / Indzhykulian, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01DC020190 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01DC017166 United States
CitationJournal: To Be Published
Title: Crystal structure of wild-type mouse gamma(S)-crystallin
Authors: Keyes, A. / De-la-Torre, P. / Indzhykulian, A.
History
DepositionNov 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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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)21,2021
Polymers21,2021
Non-polymers00
Water2,162120
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)74.056, 74.056, 79.437
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 21201.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Rosetta (plant) / References: UniProt: O35486
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, 0.5% v/v Jeffamine

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Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.83→49.95 Å / Num. obs: 38290 / % possible obs: 98.91 % / Redundancy: 2.1 % / CC1/2: 0.374 / CC star: 0.738 / Rmerge(I) obs: 0.589 / Rpim(I) all: 0.331 / Rrim(I) all: 0.678 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 2.267 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1841

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.83→49.95 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.395 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19278 1135 5 %RANDOM
Rwork0.16657 ---
obs0.16793 21452 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 1.83→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 0 120 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121586
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161391
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.6792150
X-RAY DIFFRACTIONr_angle_other_deg0.6241.5963209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.752516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62610265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9721.767737
X-RAY DIFFRACTIONr_mcbond_other1.9651.767737
X-RAY DIFFRACTIONr_mcangle_it2.7643.156926
X-RAY DIFFRACTIONr_mcangle_other2.7623.16927
X-RAY DIFFRACTIONr_scbond_it4.2562.435849
X-RAY DIFFRACTIONr_scbond_other4.2532.441850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7034.1661219
X-RAY DIFFRACTIONr_long_range_B_refined8.44528.711765
X-RAY DIFFRACTIONr_long_range_B_other8.45728.031742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.873 Å
RfactorNum. reflection% reflection
Rfree0.327 75 -
Rwork0.244 1354 -
obs--86.34 %

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