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- PDB-4jgf: Crystal Structure of the Cataract-Causing P23T gamma D-Crystallin... -

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Basic information

Entry
Database: PDB / ID: 4jgf
TitleCrystal Structure of the Cataract-Causing P23T gamma D-Crystallin Mutant
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJi, F.L. / Koharudin, L.M. / Jung, J.W. / Gronenborn, A.M.
CitationJournal: Proteins / Year: 2013
Title: Crystal structure of the cataract-causing P23T gamma D-crystallin mutant.
Authors: Ji, F. / Koharudin, L.M. / Jung, J. / Gronenborn, A.M.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)40,8092
Polymers40,8092
Non-polymers00
Water905
1
A: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,4051
Polymers20,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,4051
Polymers20,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.550, 101.931, 41.371
Angle α, β, γ (deg.)90.00, 96.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20404.705 Da / Num. of mol.: 2 / Fragment: HUMAN GAMMA D CRYSTALLIN MUTANT / Mutation: P23T
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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.93 Å3/Da / Density % sol: 36.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17 M CH3COONH4, 0.085 M C2H3NaO2 3H2O, 25.5% (w/v) PEG 4000, and 15% (v/v) glycerol , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 4, 2012
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→32.01 Å / Num. obs: 10719 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.7.0029refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.533 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28352 1055 9.8 %RANDOM
Rwork0.22773 ---
obs0.23349 9664 99.92 %-
all-10719 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0 Å2-2.98 Å2
2--0.52 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 0 5 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192940
X-RAY DIFFRACTIONr_bond_other_d0.0010.022624
X-RAY DIFFRACTIONr_angle_refined_deg0.8711.9293963
X-RAY DIFFRACTIONr_angle_other_deg0.67835981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1525341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07821.91178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.11543
X-RAY DIFFRACTIONr_chiral_restr0.060.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 72 -
Rwork0.331 720 -
obs--99.75 %

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