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- PDB-4gr7: The human W42R Gamma D-Crystallin Mutant Structure at 1.7A Resolution -

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Basic information

Entry
Database: PDB / ID: 4gr7
TitleThe human W42R Gamma D-Crystallin Mutant Structure at 1.7A Resolution
ComponentsGamma-crystallin D
KeywordsSTRUCTURAL PROTEIN / Cataract / Greek key motif / Lens fiber cell
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
PHOSPHATE ION / Gamma-crystallin D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJi, F. / Jung, J. / Koharudin, L.M.I. / Gronenborn, A.M.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: The human W42R gamma D-crystallin mutant structure provides a link between congenital and age-related cataracts.
Authors: Ji, F. / Jung, J. / Koharudin, L.M. / Gronenborn, A.M.
#1: Journal: Hum.Mutat. / Year: 2011
Title: A novel CRYGD mutation (p.Trp43Arg) causing autosomal dominant congenital cataract in a Chinese family.
Authors: Wang, B. / Yu, C. / Xi, Y.B. / Cai, H.C. / Wang, J. / Zhou, S. / Zhou, S. / Wu, Y. / Yan, Y.B. / Ma, X. / Xie, L.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,3073
Polymers41,2122
Non-polymers951
Water4,234235
1
X: Gamma-crystallin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7012
Polymers20,6061
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,6061
Polymers20,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-11 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.607, 68.607, 133.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Details2 molecules per asu

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Components

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


Mass: 20605.951 Da / Num. of mol.: 2 / Mutation: W43R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2 E. coli BL21(DE3) / References: UniProt: P07320
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.18 M Li2SO4, 0.1 M Tris-HCl, 22% (w/v) PEG 4000, 15% (v/v) glycerol , pH 8.5, VAPOR DIFFUSION, HANGING 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: May 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: 1.7→30.5 Å / Num. all: 36152 / % possible obs: 92.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.574 / % possible all: 84

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HK0

1hk0


Resolution: 1.7→30.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.695 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24458 1944 5.1 %RANDOM
Rwork0.20005 ---
obs0.20224 36152 93.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 5 235 3136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9384070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29521.749183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79815509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651546
X-RAY DIFFRACTIONr_chiral_restr0.0910.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022436
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.8461.51730
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.0322772
X-RAY DIFFRACTIONr_scbond_it6.2831285
X-RAY DIFFRACTIONr_scangle_it8.7794.51292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 108 -
Rwork0.315 2495 -
obs--87.23 %

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