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- PDB-9g3w: Human Gamma-D crystallin R36S mutant with TNB-Cystein Protein mod... -

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Basic information

Entry
Database: PDB / ID: 9g3w
TitleHuman Gamma-D crystallin R36S mutant with TNB-Cystein Protein modification
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / Greek-key / Cataract / modification / REDOX
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
5-MERCAPTO-2-NITRO-BENZOIC ACID / Gamma-crystallin D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHill, J.A. / Pulnova, Y. / Yorke, B.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Human Gamma-D crystallin R36S mutant with TNB-Cystein Protein modification
Authors: Hill, J.A. / Pulnova, Y. / Yorke, B.A.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,9628
Polymers45,7672
Non-polymers1,1956
Water1,802100
1
X: Gamma-crystallin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4814
Polymers22,8831
Non-polymers5983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Gamma-crystallin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4814
Polymers22,8831
Non-polymers5983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.800, 83.500, 100.700
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: 22883.420 Da / Num. of mol.: 2 / Mutation: R36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07320
#2: Chemical
ChemComp-MNB / 5-MERCAPTO-2-NITRO-BENZOIC ACID


Mass: 199.184 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H5NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.8 / Details: 50 mM phosphate buffer pH 7.8

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESC / Wavelength: 1.02 Å
DetectorType: PSI JUNGFRAU 8M / Detector: PIXEL / Date: Mar 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.152→36.633 Å / Num. obs: 115699 / % possible obs: 100 % / Redundancy: 139 % / CC1/2: 0.9574345 / Net I/σ(I): 1.17
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 131 % / Num. unique obs: 4605 / CC1/2: 0.18 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
CrystFELdata scaling
CrystFELdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.999 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24334 2143 5 %RANDOM
Rwork0.19989 ---
obs0.20199 42864 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20 Å2
2---0.18 Å20 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.8→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 78 100 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162638
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.8284115
X-RAY DIFFRACTIONr_angle_other_deg0.5921.786021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.314552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69110489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02859
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_it2.2342.5691384
X-RAY DIFFRACTIONr_mcbond_other2.2332.5691384
X-RAY DIFFRACTIONr_mcangle_it3.1994.5771731
X-RAY DIFFRACTIONr_mcangle_other3.1984.581732
X-RAY DIFFRACTIONr_scbond_it4.4683.4731660
X-RAY DIFFRACTIONr_scbond_other4.4573.4641656
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1266.0192381
X-RAY DIFFRACTIONr_long_range_B_refined9.21328.683508
X-RAY DIFFRACTIONr_long_range_B_other9.20628.693500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 136 -
Rwork0.346 2981 -
obs--100 %

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