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- PDB-6eta: Crystal Structure of Human Gamma-D crystallin Mutant P23T+R36S at... -

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Basic information

Entry
Database: PDB / ID: 6eta
TitleCrystal Structure of Human Gamma-D crystallin Mutant P23T+R36S at Room Temperature
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / age-related cateract eye lens protein structural protein
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
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsJames, S. / McManus, J. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation IrelandSFI 12/1A/1239 Ireland
CitationJournal: Biophys.J. / Year: 2019
Title: Temperature-Dependent Interactions Explain Normal and Inverted Solubility in a gamma D-Crystallin Mutant.
Authors: Khan, A.R. / James, S. / Quinn, M.K. / Altan, I. / Charbonneau, P. / McManus, J.J.
History
DepositionOct 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: 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 1.2Jan 17, 2024Group: 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
B: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)41,4002
Polymers41,4002
Non-polymers00
Water2,018112
1
A: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,7001
Polymers20,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,7001
Polymers20,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.036, 82.103, 106.248
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: 20700.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli (E. coli) / References: UniProt: P07320
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7 / Details: 0.1M phosphate, 20mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.198→48.165 Å / Num. obs: 24656 / % possible obs: 99.63 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.139 / Net I/σ(I): 9.2
Reflection shellResolution: 2.198→2.27 Å / Rmerge(I) obs: 1.29 / Rrim(I) all: 1.43

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jgf

4jgf


Resolution: 2.198→48.165 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.36
RfactorNum. reflection% reflection
Rfree0.2648 1233 5 %
Rwork0.2328 --
obs0.2344 24656 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.198→48.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 0 112 2888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032846
X-RAY DIFFRACTIONf_angle_d0.73844
X-RAY DIFFRACTIONf_dihedral_angle_d3.0541666
X-RAY DIFFRACTIONf_chiral_restr0.046377
X-RAY DIFFRACTIONf_plane_restr0.004509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1985-2.28650.34371320.2952522X-RAY DIFFRACTION98
2.2865-2.39060.32111340.28382555X-RAY DIFFRACTION100
2.3906-2.51660.32711340.27932555X-RAY DIFFRACTION99
2.5166-2.67430.31641360.27622574X-RAY DIFFRACTION100
2.6743-2.88070.31991370.2632591X-RAY DIFFRACTION100
2.8807-3.17060.2651360.24362601X-RAY DIFFRACTION100
3.1706-3.62920.24871380.21812613X-RAY DIFFRACTION100
3.6292-4.57190.22041390.19482641X-RAY DIFFRACTION100
4.5719-48.17630.25881470.22652771X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.6744 Å / Origin y: 91.3059 Å / Origin z: -7.3998 Å
111213212223313233
T0.2906 Å2-0.037 Å2-0.0331 Å2-0.3782 Å2-0.1149 Å2--0.3857 Å2
L1.0347 °2-0.8909 °2-1.0417 °2-0.7645 °20.3947 °2--0.6648 °2
S0.0005 Å °0.352 Å °-0.3658 Å °-0.046 Å °-0.231 Å °0.3113 Å °0.0919 Å °-0.2962 Å °0.0857 Å °
Refinement TLS groupSelection details: all

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