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- PDB-7p53: Crystal Structure of Human gamma-D-crystallin mutant C110M at 1.5... -

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Basic information

Entry
Database: PDB / ID: 7p53
TitleCrystal Structure of Human gamma-D-crystallin mutant C110M at 1.57 Angstroms resolution
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / Cysteine mutation / Recombinant / Eye lens
Function / homology
Function and homology information


lens fiber cell differentiation / structural constituent of eye lens / lens development in camera-type eye / visual perception / cellular response to reactive oxygen species / nucleus / cytoplasm
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: 1.57 Å
AuthorsStrofaldi, A. / Khan, A.R. / McManus, J.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Other governmentBU1300037 Ireland
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Surface Exposed Free Cysteine Suppresses Crystallization of Human gamma D-Crystallin.
Authors: Strofaldi, A. / Khan, A.R. / McManus, J.J.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
X: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,6631
Polymers20,6631
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, In the conditions used for experiments the protein is monomeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.699, 52.844, 89.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Gamma-crystallin D / Gamma-D-crystallin / Gamma-crystallin 4


Mass: 20663.021 Da / Num. of mol.: 1 / Mutation: C110M
Source method: isolated from a genetically manipulated source
Details: The protein is a mutant of Human gamma-D crystallin where the 110th cysteine is replaced by a methionine (C110M).
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Organ: Eye / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21-Gold(DE3) / References: UniProt: P07320
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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 % / Description: Rhombic crystals.
Crystal growTemperature: 277 K / Method: batch mode / pH: 7
Details: Crystals were obtained in 0.1M Sodium Phosphate Buffer pH 7 inducing LLPS at approximately 263K for 3hours from 150mg/mL solutions. Crystals were observed after few hours of incubation at 277K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.57→52.84 Å / Num. obs: 22817 / % possible obs: 99.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.083 / Rrim(I) all: 0.206 / Net I/σ(I): 6
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.941 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 953 / Rpim(I) all: 0.883 / Rrim(I) all: 2.141 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hk0

1hk0


Resolution: 1.57→45.51 Å / SU ML: 0.3044 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2738 1126 5.02 %
Rwork0.2147 21297 -
obs0.2175 22423 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.55 Å2
Refinement stepCycle: LAST / Resolution: 1.57→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 0 108 1561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961506
X-RAY DIFFRACTIONf_angle_d1.06662029
X-RAY DIFFRACTIONf_chiral_restr0.0594191
X-RAY DIFFRACTIONf_plane_restr0.0191271
X-RAY DIFFRACTIONf_dihedral_angle_d14.1589570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.640.43181200.43992265X-RAY DIFFRACTION85.15
1.64-1.730.46921570.37752651X-RAY DIFFRACTION99.33
1.73-1.840.33211420.33082661X-RAY DIFFRACTION99.43
1.84-1.980.36951400.29042693X-RAY DIFFRACTION99.47
1.98-2.180.34381320.24192676X-RAY DIFFRACTION99.33
2.18-2.50.25381490.20312706X-RAY DIFFRACTION99.83
2.5-3.150.26121360.20042768X-RAY DIFFRACTION99.93
3.15-45.510.22041500.17082877X-RAY DIFFRACTION99.44

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