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- PDB-1hk0: Human GammaD Crystallin Structure at 1.25 A Resolution -

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Basic information

Entry
Database: PDB / ID: 1hk0
TitleHuman GammaD Crystallin Structure at 1.25 A Resolution
ComponentsGamma-crystallin D
KeywordsEYE LENS PROTEIN / CATARACT
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBasak, A.K. / Slingsby, C.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: High-Resolution X-Ray Crystal Structures of Human Gammad Crystallin (1.25A) and the R58H Mutant (1.15A) Associated with Aculeiform Cataract
Authors: Basak, A.K. / Bateman, O. / Slingsby, C. / Pande, A. / Asherie, N. / Ogun, O. / Benedek, G. / Pande, J.
#1: Journal: Exp.Eye Res. / Year: 1991
Title: Crystal Structure of Calf Eye Lens Gamma-Crystallin Iiib at 2.5 A Resolution: Its Relation to Function
Authors: Yu, C. / Nevskaya, N. / Vernoslova, E. / Nikonov, S. / Yu, S. / Brazhnikov, E. / Fomenkova, N. / Lunin, V. / Urzhumtsev, A.
History
DepositionMar 5, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / exptl_crystal_grow / pdbx_entity_src_syn / struct / struct_ref / struct_ref_seq
Item: _citation.page_last / _entity.pdbx_description ..._citation.page_last / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _exptl_crystal_grow.temp / _struct.title / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Gamma-crystallin D


Theoretical massNumber of molelcules
Total (without water)20,6351
Polymers20,6351
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.220, 52.971, 90.468
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: 20634.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P07320
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 1.87 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 277 K / pH: 7 / Details: 10MM PHOSPHATE, 4 DEGREE CELSIUS, pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium phosphate11pH7.
220 mldithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2001 / Details: MIRROR
RadiationMonochromator: LAUE DIAMOND C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.25→28.17 Å / Num. obs: 39066 / % possible obs: 86.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 7.4
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.7 / % possible all: 45.5
Reflection
*PLUS
Num. obs: 39021 / Num. measured all: 212732
Reflection shell
*PLUS
% possible obs: 45.5 % / Redundancy: 1.9 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ELP

1elp


Resolution: 1.25→28.17 Å / SU B: 0.877 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3238 8.3 %RANDOM
Rwork0.164 ---
obs0.167 35783 86.84 %-
Displacement parametersBiso mean: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---1.14 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.25→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 0 282 1729
Refinement
*PLUS
% reflection Rfree: 8 % / Rfactor obs: 0.1671 / Rfactor Rfree: 0.2078 / Rfactor Rwork: 0.1636
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.786
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.529

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