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- PDB-8bpi: Human Gamma-D crystallin R36S mutant after UV illumination -

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Basic information

Entry
Database: PDB / ID: 8bpi
TitleHuman Gamma-D crystallin R36S mutant after UV illumination
Components(Gamma-crystallin D) x 2
KeywordsSTRUCTURAL PROTEIN / UV exposure / oxidisation / 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 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
DepositionNov 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
XXX: Gamma-crystallin D
AAA: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)43,6442
Polymers43,6442
Non-polymers00
Water1,44180
1
XXX: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)21,8141
Polymers21,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)21,8301
Polymers21,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.900, 83.700, 101.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11XXX
21AAA

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 172 / Label seq-ID: 10 - 181

Dom-IDAuth asym-IDLabel asym-ID
1XXXA
2AAAB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 21814.240 Da / Num. of mol.: 1 / Mutation: R36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Plasmid: pET30b(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07320
#2: Protein Gamma-crystallin D / Gamma-D-crystallin / Gamma-crystallin 4


Mass: 21830.240 Da / Num. of mol.: 1 / Mutation: R36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Plasmid: pET30b(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07320
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 % / 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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→101 Å / Num. obs: 31633 / % possible obs: 100 % / Redundancy: 70.2 % / CC1/2: 0.9546 / CC star: 0.9883 / R split: 0.2277 / Net I/σ(I): 3.19
Reflection shellResolution: 2→2.07 Å / Redundancy: 48.3 % / Mean I/σ(I) obs: 0.68 / Num. unique obs: 3090 / CC1/2: 0.2283 / CC star: 0.6096 / R split: 1.669 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography data reductionFrames indexed: 25600

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G98

2g98


Resolution: 2→101 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.722 / SU ML: 0.164 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2407 1746 6.455 %
Rwork0.1973 25303 -
all0.2 --
obs-27049 85.666 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.682 Å20 Å2-0 Å2
2--0.323 Å2-0 Å2
3---0.358 Å2
Refinement stepCycle: LAST / Resolution: 2→101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 0 80 2951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142646
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6494067
X-RAY DIFFRACTIONr_angle_other_deg1.241.5856051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.71219.781228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43915498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9031543
X-RAY DIFFRACTIONr_chiral_restr0.0680.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
X-RAY DIFFRACTIONr_nbd_refined0.1740.2488
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22509
X-RAY DIFFRACTIONr_nbtor_refined0.170.21361
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.28
X-RAY DIFFRACTIONr_nbd_other0.1790.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.27
X-RAY DIFFRACTIONr_mcbond_it2.5553.4951388
X-RAY DIFFRACTIONr_mcbond_other2.5413.4911387
X-RAY DIFFRACTIONr_mcangle_it3.8485.2311736
X-RAY DIFFRACTIONr_mcangle_other3.8485.2361737
X-RAY DIFFRACTIONr_scbond_it3.924.191625
X-RAY DIFFRACTIONr_scbond_other3.9194.1931626
X-RAY DIFFRACTIONr_scangle_it6.3816.052329
X-RAY DIFFRACTIONr_scangle_other6.386.0542330
X-RAY DIFFRACTIONr_lrange_it9.47468.68912435
X-RAY DIFFRACTIONr_lrange_other9.47368.62712406
X-RAY DIFFRACTIONr_ncsr_local_group_10.0860.055854
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11XXXX-RAY DIFFRACTIONLocal ncs0.086490.0501
12AAAX-RAY DIFFRACTIONLocal ncs0.086490.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.3651050.3771481X-RAY DIFFRACTION69.7449
2.052-2.1080.3641170.3531522X-RAY DIFFRACTION73.4319
2.108-2.1690.3781020.3331540X-RAY DIFFRACTION74.7043
2.169-2.2360.3311170.3051529X-RAY DIFFRACTION78.2691
2.236-2.3090.2951110.2851557X-RAY DIFFRACTION80.814
2.309-2.390.2961120.2911483X-RAY DIFFRACTION80.0703
2.39-2.480.3681140.2891519X-RAY DIFFRACTION84.3056
2.48-2.5820.342910.261485X-RAY DIFFRACTION85.2353
2.582-2.6960.3411050.2711453X-RAY DIFFRACTION87.0878
2.696-2.8280.299950.2421437X-RAY DIFFRACTION89.8534
2.828-2.9810.249880.1931432X-RAY DIFFRACTION92.7961
2.981-3.1610.265830.1941375X-RAY DIFFRACTION94.5525
3.161-3.3790.248880.1661315X-RAY DIFFRACTION95.5722
3.379-3.650.168940.1511223X-RAY DIFFRACTION97.3392
3.65-3.9980.174730.1341162X-RAY DIFFRACTION97.6285
3.998-4.4690.159620.1331035X-RAY DIFFRACTION96.0595
4.469-5.1580.151580.112939X-RAY DIFFRACTION97.7451
5.158-6.3130.197500.14809X-RAY DIFFRACTION97.0621
6.313-8.9110.252480.176630X-RAY DIFFRACTION96.8571
8.911-1010.178330.184377X-RAY DIFFRACTION97.852

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