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- PDB-1zir: Deuterated gammaE crystallin in H2O solvent -

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Basic information

Entry
Database: PDB / ID: 1zir
TitleDeuterated gammaE crystallin in H2O solvent
ComponentsGamma crystallin E
KeywordsSTRUCTURAL PROTEIN / 4 Greek key motifs
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
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
ACETATE ION / Gamma-crystallin E
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsArtero, J.B. / Hartlein, M. / McSweeney, S. / Timmins, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: A comparison of refined X-ray structures of hydrogenated and perdeuterated rat gammaE-crystallin in H2O and D2O.
Authors: Artero, J.B. / Hartlein, M. / McSweeney, S. / Timmins, P.
History
DepositionApr 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Gamma crystallin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3414
Polymers21,1641
Non-polymers1773
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.530, 43.320, 101.610
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 E / Gamma crystallin 3-1 / Gamma-2


Mass: 21163.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02528
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 3350, Magnesium acetate, H2O, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2003
RadiationMonochromator: a double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.36→50.64 Å / Num. all: 36549 / Num. obs: 36512 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.36→1.45 Å / % possible all: 93.7

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Processing

Software
NameClassification
MOSFLMdata reduction
XDSdata reduction
MOLREPphasing
SHELXL-97refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A5D

1a5d


Resolution: 1.36→50.64 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.211 1593 Random
Rwork0.18 --
all0.187 36512 -
obs0.182 36483 -
Refinement stepCycle: LAST / Resolution: 1.36→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 12 147 1771
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d1.768

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