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- PDB-4fd9: Crystal structure of the third beta-gamma-crystallin domain of Cr... -

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Basic information

Entry
Database: PDB / ID: 4fd9
TitleCrystal structure of the third beta-gamma-crystallin domain of Crybg3 (betagamma-crystallin domain-containing protein 3) from Mus musculus
ComponentsBeta/gamma crystallin domain-containing protein 3
KeywordsSTRUCTURAL PROTEIN / Non-lens vertebrate beta-gamma-crystallin / Brain
Function / homology
Function and homology information


eye development / carbohydrate binding
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 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil ...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 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta/gamma crystallin domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAravind, P. / Srivastava, S.S. / Sankaranarayanan, R.
CitationJournal: Biochemistry / Year: 2012
Title: Aggregation-prone near-native intermediate formation during unfolding of a structurally similar nonlenticular beta/gamma-crystallin domain
Authors: Rajanikanth, V. / Srivastava, S.S. / Singh, A.K. / Rajyalakshmi, M. / Chandra, K. / Aravind, P. / Sankaranarayanan, R. / Sharma, Y.
History
DepositionMay 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Beta/gamma crystallin domain-containing protein 3
B: Beta/gamma crystallin domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)20,8702
Polymers20,8702
Non-polymers00
Water3,783210
1
A: Beta/gamma crystallin domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)10,4351
Polymers10,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta/gamma crystallin domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)10,4351
Polymers10,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.261, 58.808, 40.995
Angle α, β, γ (deg.)90.00, 118.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta/gamma crystallin domain-containing protein 3


Mass: 10434.805 Da / Num. of mol.: 2 / Fragment: beta-gamma-crystallin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Tissue: Brain / Gene: Crybg3 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q80W49
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-25% PEG 4K, 0.1M Na Hepes, 10% isopropanol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.606
11-H, -K, H+L20.394
ReflectionResolution: 1.86→25 Å / Num. obs: 13629 / Redundancy: 5.7 % / Rmerge(I) obs: 0.037
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 5 % / Rmerge(I) obs: 0.2 / Num. unique all: 1167

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.automr)model building
REFMAC5.7.0025refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→22.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.774 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17904 673 4.9 %RANDOM
Rwork0.13631 ---
obs0.1385 12940 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.189 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å21.43 Å2
2--8.4 Å20 Å2
3----6.9 Å2
Refinement stepCycle: LAST / Resolution: 1.86→22.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 0 210 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221512
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9392032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26224.32474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16715260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.106154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211156
LS refinement shellResolution: 1.865→1.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 45 -
Rwork0.239 844 -
obs--92.32 %

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