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- PDB-1ha4: GammaS crystallin C terminal domain from Homo Sapiens -

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Basic information

Entry
Database: PDB / ID: 1ha4
TitleGammaS crystallin C terminal domain from Homo Sapiens
ComponentsGAMMA CRYSTALLIN S
KeywordsEYE LENS PROTEIN / GAMMAS CRYSTALLIN
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
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: 2.4 Å
AuthorsPurkiss, A.G. / Slingsby, C. / Bateman, O.A. / Goodfellow, J.M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The X-Ray Crystal Structure of Human Gamma S-Crystallin C-Terminal Domain
Authors: Purkiss, A.G. / Bateman, O.A. / Goodfellow, J.M. / Lubsen, N.H. / Slingsby, C.
History
DepositionMar 27, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMA CRYSTALLIN S
B: GAMMA CRYSTALLIN S


Theoretical massNumber of molelcules
Total (without water)20,8562
Polymers20,8562
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.367, 61.367, 241.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein GAMMA CRYSTALLIN S / BETA CRYSTALLIN S


Mass: 10427.862 Da / Num. of mol.: 2 / Fragment: C TERMINAL DOMAIN RESIDUES 91-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASM / Organ: EYE / Organelle: EYE-LENS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22914
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 6.308 Å3/Da / Density % sol: 61 %
Crystal growpH: 5
Details: 0.1M SODIUM ACETATE, 0.2M AMMONIUM SULPHATE, 24% PEG MONOMETHYLETHER, pH 5.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 mMBis-Tris propane-HCl1droppH7.5
30.2 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoirpH5.0
524 %PEG2000MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.5418
DetectorDate: Mar 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→48.7 Å / Num. obs: 10955 / % possible obs: 97.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.439 Å2 / Rsym value: 0.057 / Net I/σ(I): 23.8
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 5.7 / Rsym value: 0.107 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 71559 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.4 % / Num. unique obs: 809 / Num. measured obs: 4790 / Rmerge(I) obs: 0.107

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Processing

Software
NameVersionClassification
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A7H

1a7h


Resolution: 2.4→100 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: ALSO USED CCP4 PROGRAMS REFMAC, FFT, MAPMASK AND ARPP FOR SOME REFINEMENT ROUNDS
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 844 7.4 %RANDOM
Rwork0.2159 ---
obs0.2159 10965 99.4 %-
Solvent computationSolvent model: SHELL MODEL / Bsol: 49.795 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 30.904 Å2
Baniso -1Baniso -2Baniso -3
1--1.521 Å2-6.423 Å20 Å2
2---1.521 Å20 Å2
3---3.042 Å2
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 0 90 1558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0093
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.388
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.107 819 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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