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- PDB-8q3l: Human Gamma-D Crystallin R36S fresh serial crystallographic structure -

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Basic information

Entry
Database: PDB / ID: 8q3l
TitleHuman Gamma-D Crystallin R36S fresh serial crystallographic structure
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / eye lens 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
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: 2.1 Å
AuthorsYorke, B.A. / Hill, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustSBF0061044 United Kingdom
CitationJournal: Commun Chem / Year: 2024
Title: An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin.
Authors: Hill, J.A. / Nyathi, Y. / Horrell, S. / von Stetten, D. / Axford, D. / Owen, R.L. / Beddard, G.S. / Pearson, A.R. / Ginn, H.M. / Yorke, B.A.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Gamma-crystallin D
A: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)43,5642
Polymers43,5642
Non-polymers00
Water1,33374
1
X: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)21,7821
Polymers21,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)21,7821
Polymers21,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.600, 83.700, 100.400
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


Mass: 21782.238 Da / Num. of mol.: 2 / Mutation: R36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD / Plasmid: pET30b(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07320
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.58 Å3/Da / Density % sol: 52.41 % / Description: microcrystalline plate-like
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.8 / Details: 50 mM phosphate buffer pH 7.8, 20 mM DTT / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.1→38.66 Å / Num. obs: 50856 / % possible obs: 99.9 % / Redundancy: 26.7 % / CC1/2: 0.974 / CC star: 0.994 / R split: 0.19 / Net I/σ(I): 3.87
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2844 / CC1/2: 0.49 / CC star: 0.811 / R split: 1.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
CrystFELdata scaling
CrystFELdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.66 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.729 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25783 1317 4.9 %RANDOM
Rwork0.2037 ---
obs0.20624 25669 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.1→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 0 74 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162640
X-RAY DIFFRACTIONr_angle_refined_deg1.451.6764082
X-RAY DIFFRACTIONr_angle_other_deg0.5061.5926037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8995355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.232541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4210497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02866
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_it3.0413.3771405
X-RAY DIFFRACTIONr_mcbond_other3.0343.3781405
X-RAY DIFFRACTIONr_mcangle_it4.486.0361762
X-RAY DIFFRACTIONr_mcangle_other4.4816.0411763
X-RAY DIFFRACTIONr_scbond_it5.0464.2091614
X-RAY DIFFRACTIONr_scbond_other5.0444.2141615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8977.3592320
X-RAY DIFFRACTIONr_long_range_B_refined11.2843.7112842
X-RAY DIFFRACTIONr_long_range_B_other11.28343.6312820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 94 -
Rwork0.388 1866 -
obs--99.34 %

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