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- PDB-7rj0: Mouse Gamma S Crystallin L16 Octamer -

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Basic information

Entry
Database: PDB / ID: 7rj0
TitleMouse Gamma S Crystallin L16 Octamer
ComponentsGamma-crystallin S
KeywordsSTRUCTURAL PROTEIN / Octamer / Domain-swap / Oxidation / Disorder / PROTEIN BINDING
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.919 Å
AuthorsSagar, V.
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Acquired Disorder and Asymmetry in a Domain-Swapped Model for gamma-Crystallin Aggregation.
Authors: Sagar, V. / Wistow, G.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionApr 13, 2022ID: 6MYH
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Gamma-crystallin S
A: Gamma-crystallin S
C: Gamma-crystallin S
D: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)83,6804
Polymers83,6804
Non-polymers00
Water1,24369
1
B: Gamma-crystallin S
A: Gamma-crystallin S
C: Gamma-crystallin S
D: Gamma-crystallin S

B: Gamma-crystallin S
A: Gamma-crystallin S
C: Gamma-crystallin S
D: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)167,3598
Polymers167,3598
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area18860 Å2
ΔGint-89 kcal/mol
Surface area61540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.095, 77.591, 154.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

21D-210-

HOH

31D-211-

HOH

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Components

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


Mass: 20919.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crygs / Production host: Escherichia coli (E. coli) / References: UniProt: O35486
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.15 M sodium acetate, pH 5.0, 22% PEG550 MME, 8% PEG300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16343 / % possible obs: 99.3 % / Redundancy: 10 % / Rsym value: 0.158 / Net I/σ(I): 25
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 800 / Rsym value: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZWO

1zwo


Resolution: 2.919→48.001 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 32.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2897 850 5.21 %
Rwork0.1989 15457 -
obs0.2039 16307 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.13 Å2 / Biso mean: 89.9 Å2 / Biso min: 32.61 Å2
Refinement stepCycle: final / Resolution: 2.919→48.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 0 69 5520
Biso mean---75.46 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115712
X-RAY DIFFRACTIONf_angle_d1.2937757
X-RAY DIFFRACTIONf_chiral_restr0.065774
X-RAY DIFFRACTIONf_plane_restr0.0091030
X-RAY DIFFRACTIONf_dihedral_angle_d21.2663343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.919-3.10160.35991210.2478243595
3.1016-3.3410.33941440.20922555100
3.341-3.67710.29221310.18782582100
3.6771-4.20890.28031420.1848257499
4.2089-5.30170.24281480.1665259098
5.3017-48.0010.31021640.2276272198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.7079-2.09872.13527.1067-0.16089.19490.0954-0.35171.3060.40590.128-0.4449-0.4668-0.0363-0.14970.4598-0.07770.09110.3887-0.08430.545816.6885-21.477-37.3954
28.2897-0.3203-1.27779.5773-3.33419.62870.12610.31810.3701-0.6396-0.0851-0.2382-1.1737-0.2447-0.1040.7955-0.0511-0.04170.43820.0390.3234-12.9953-19.2465-72.2276
38.7309-1.30942.33996.6285-5.29989.48650.08210.3634-0.0393-0.6645-0.5262-0.5672-0.06250.36020.29260.79390.00290.12190.4494-0.0160.484818.7746-7.1442-57.4572
44.74011.5688-1.50538.1232-0.469810.1084-0.21670.55430.035-0.66630.68160.3350.3994-0.4015-0.43730.4904-0.0829-0.05130.4640.09260.2682-15.6734-38.9853-57.2129
59.81780.01493.35066.94651.33748.8110.1556-0.08371.05150.14170.12520.1659-0.4409-0.265-0.28910.48190.02560.13840.34610.04570.4856-14.1978-19.1551-39.3314
69.1279-1.16260.05749.35762.23634.46740.3155-0.52770.44210.9416-0.31110.1424-1.49050.4439-0.01291.5021-0.18760.02180.9331-0.18870.530414.2749-21.2509-5.1075
77.5732-1.7613-1.01978.73431.22624.9783-0.3056-1.5284-0.16771.52990.5594-0.44020.1945-0.0581-0.22620.76640.021-0.06970.692-0.01170.354515.1916-40.6375-19.8576
83.38340.3592-0.13856.94543.99059.02850.0794-0.76492.57912.45070.206-0.2352-1.0173-0.3502-0.39981.75970.03450.20660.8222-0.17081.3664-14.7756-5.405-18.4914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and ((resseq 3:85))B3 - 85
2X-RAY DIFFRACTION2chain 'B' and ((resseq 93:177))B93 - 177
3X-RAY DIFFRACTION3chain 'A' and ((resseq 93:177))A93 - 177
4X-RAY DIFFRACTION4chain 'A' and ((resseq 4:85))A4 - 85
5X-RAY DIFFRACTION5chain 'C' and ((resseq 4:85))C4 - 85
6X-RAY DIFFRACTION6chain 'C' and ((resseq 93:177))C93 - 177
7X-RAY DIFFRACTION7chain 'D' and ((resseq 4:85))D4 - 85
8X-RAY DIFFRACTION8chain 'D' and ((resseq 93:177))D93 - 177

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