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- PDB-1m8u: Crystal Structure of Bovine gamma-E at 1.65 Ang Resolution -

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Basic information

Entry
Database: PDB / ID: 1m8u
TitleCrystal Structure of Bovine gamma-E at 1.65 Ang Resolution
Componentsgamma-E
KeywordsSTRUCTURAL PROTEIN / gamma-crystallin / gamma-E
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMayer, C. / Agueznay, N. / Skouri-Panet, F. / Prat, K. / Putilina, T. / Biarrotte-Sorin, S. / Tardieu, A.
CitationJournal: To be Published
Title: Crystal Structure of Bovine gamma-E
Authors: Mayer, C. / Agueznay, N. / Skouri-Panet, F. / Prat, K. / Putilina, T. / Biarrotte-Sorin, S. / Tardieu, A.
History
DepositionJul 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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-E


Theoretical massNumber of molelcules
Total (without water)21,0621
Polymers21,0621
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.800, 36.710, 46.250
Angle α, β, γ (deg.)100.06, 106.92, 105.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein gamma-E


Mass: 21062.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: extracted from calf eye lens / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P23005
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.5
Details: PEG 3000, sodium acetate, pH 4.5, microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 13, 2002
RadiationMonochromator: mirror + double crystal + mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.65→28 Å / Num. obs: 20771 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 11.4 Å2 / Rsym value: 0.051 / Net I/σ(I): 8
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1518 / Rsym value: 0.104 / % possible all: 79.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A5D

1a5d


Resolution: 1.65→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 932 5 %RANDOM
Rwork0.186 ---
obs-19708 91 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.423 Å20.281 Å2-0.5 Å2
2--0.591 Å2-0.292 Å2
3----1.014 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 0 315 1802
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.05
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.4642
X-RAY DIFFRACTIONc_scbond_it1.9532
X-RAY DIFFRACTIONc_scangle_it2.7642.5
LS refinement shellResolution: 1.65→1.71 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.232 89 5 %
Rwork0.223 1496 -
obs--0.74 %

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