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- PDB-8bd0: Human Gamma-D crystallin R36S mutant with DTT-Cystein Protein mod... -

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Basic information

Entry
Database: PDB / ID: 8bd0
TitleHuman Gamma-D crystallin R36S mutant with DTT-Cystein Protein modification
ComponentsHuman Gamma-D Crystallin R36S
KeywordsSTRUCTURAL PROTEIN / chemical modification / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Gamma-crystallin D
Similarity search - Component
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
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2May 15, 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 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
X: Human Gamma-D Crystallin R36S
A: Human Gamma-D Crystallin R36S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3106
Polymers40,6932
Non-polymers6174
Water1,45981
1
X: Human Gamma-D Crystallin R36S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6553
Polymers20,3471
Non-polymers3092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Human Gamma-D Crystallin R36S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6553
Polymers20,3471
Non-polymers3092
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.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Human Gamma-D Crystallin R36S


Mass: 20346.600 Da / Num. of mol.: 2 / Mutation: R36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30b(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07320
#2: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.8 Å3/Da / Density % sol: 56.07 % / 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 1M / 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→101.13 Å / Num. obs: 31629 / % possible obs: 99.99 % / Redundancy: 50.3 % / CC1/2: 0.9956 / CC star: 0.982 / R split: 0.2717 / Net I/σ(I): 2.71
Reflection shellResolution: 2→2.07 Å / Redundancy: 34.7 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3090 / CC1/2: 0.14 / CC star: 0.5062 / R split: 1.94 / % 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: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.358 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24971 1718 6.4 %RANDOM
Rwork0.20437 ---
obs0.20727 25054 84.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0 Å2
2--0.26 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 2→101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 32 81 2971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133016
X-RAY DIFFRACTIONr_bond_other_d0.0040.0152655
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.6524063
X-RAY DIFFRACTIONr_angle_other_deg1.2381.5926067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07819.955222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77815492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.741541
X-RAY DIFFRACTIONr_chiral_restr0.0670.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
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_it2.3113.3411386
X-RAY DIFFRACTIONr_mcbond_other2.3053.3391385
X-RAY DIFFRACTIONr_mcangle_it3.4464.9991734
X-RAY DIFFRACTIONr_mcangle_other3.4475.0031735
X-RAY DIFFRACTIONr_scbond_it3.8874.0461630
X-RAY DIFFRACTIONr_scbond_other3.8864.0491631
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0415.8392328
X-RAY DIFFRACTIONr_long_range_B_refined9.31766.4312484
X-RAY DIFFRACTIONr_long_range_B_other9.31866.4412463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 115 -
Rwork0.401 1446 -
obs--68.65 %

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