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- PDB-6w5b: N124D Deamidation Mutant of Human gammaD-Crystallin -

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Basic information

Entry
Database: PDB / ID: 6w5b
TitleN124D Deamidation Mutant of Human gammaD-Crystallin
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / deamidation / lens / cataract / protein modification
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: 1.15 Å
AuthorsWhitley, M.J. / Rathi, N. / Ambarian, M. / Gronenborn, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY030057 United States
CitationJournal: Structure / Year: 2021
Title: Assessing the Structures and Interactions of gamma D-Crystallin Deamidation Variants.
Authors: Guseman, A.J. / Whitley, M.J. / Gonzalez, J.J. / Rathi, N. / Ambarian, M. / Gronenborn, A.M.
History
DepositionMar 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,6361
Polymers20,6361
Non-polymers00
Water3,477193
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)33.649, 51.493, 93.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20635.955 Da / Num. of mol.: 1 / Mutation: N125D
Source method: isolated from a genetically manipulated source
Details: No electron density for the last three residues. / Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07320
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.15→28.17 Å / Num. obs: 58473 / % possible obs: 99.32 % / Redundancy: 11.6 % / Biso Wilson estimate: 12.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Net I/σ(I): 17.43
Reflection shellResolution: 1.15→1.191 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5481 / CC1/2: 0.866 / Rpim(I) all: 0.2414 / Rrim(I) all: 0.5748 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HK0

1hk0


Resolution: 1.15→28.17 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.14
Details: Anisotropic ADPs refined for all non-hydrogen protein atoms. Explicit riding hydrogens added to model for refinement.
RfactorNum. reflection% reflection
Rfree0.1722 2924 5 %
Rwork0.1509 --
obs0.152 58458 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.15→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1425 0 0 193 1618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111530
X-RAY DIFFRACTIONf_angle_d1.2142077
X-RAY DIFFRACTIONf_dihedral_angle_d13.158225
X-RAY DIFFRACTIONf_chiral_restr0.105199
X-RAY DIFFRACTIONf_plane_restr0.008278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.170.21841260.18882388X-RAY DIFFRACTION90
1.17-1.190.20461330.17432540X-RAY DIFFRACTION97
1.19-1.210.21461370.16332591X-RAY DIFFRACTION99
1.21-1.230.21441380.14822623X-RAY DIFFRACTION100
1.23-1.260.17231390.14162639X-RAY DIFFRACTION100
1.26-1.290.1841390.13822638X-RAY DIFFRACTION100
1.29-1.320.16611370.12932593X-RAY DIFFRACTION100
1.32-1.350.16921400.12832662X-RAY DIFFRACTION100
1.35-1.390.16951370.12432612X-RAY DIFFRACTION100
1.39-1.430.16561390.12722638X-RAY DIFFRACTION100
1.43-1.470.17161400.13032650X-RAY DIFFRACTION100
1.47-1.520.16351380.12732633X-RAY DIFFRACTION100
1.52-1.590.15241400.12482649X-RAY DIFFRACTION100
1.59-1.660.14781400.12812662X-RAY DIFFRACTION100
1.66-1.750.16211390.12952656X-RAY DIFFRACTION100
1.75-1.850.17861410.13982662X-RAY DIFFRACTION100
1.85-20.15991410.13762682X-RAY DIFFRACTION100
2-2.20.17061410.14042680X-RAY DIFFRACTION100
2.2-2.520.17121420.14932710X-RAY DIFFRACTION100
2.52-3.170.19151450.17282740X-RAY DIFFRACTION100
3.17-28.170.16751520.17132886X-RAY DIFFRACTION100

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