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- PDB-3eyb: Structural and functional insights into the ligand binding domain... -

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Basic information

Entry
Database: PDB / ID: 3eyb
TitleStructural and functional insights into the ligand binding domain of a non-duplicated RXR from the invertebrate chordate amphioxus
ComponentsNuclear hormone receptor RXR
KeywordsTRANSCRIPTION / Amphioxus / Retinoid X receptor / nuclear receptor / ligand binding / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


nuclear steroid receptor activity / sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus
Similarity search - Function
Retinoid X receptor/HNF4 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...Retinoid X receptor/HNF4 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear hormone receptor RXR
Similarity search - Component
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsTocchini-Valentini, G.D. / Rochel, N. / Moras, D. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and functional insights into the ligand-binding domain of a nonduplicated retinoid X nuclear receptor from the invertebrate chordate amphioxus
Authors: Tocchini-Valentini, G.D. / Rochel, N. / Escriva, H. / Germain, P. / Peluso-Iltis, C. / Paris, M. / Sanglier-Cianferani, S. / Van Dorsselaer, A. / Moras, D. / Laudet, V.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Nuclear hormone receptor RXR
B: Nuclear hormone receptor RXR
C: Nuclear hormone receptor RXR
D: Nuclear hormone receptor RXR


Theoretical massNumber of molelcules
Total (without water)98,7914
Polymers98,7914
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-23 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.723, 96.120, 131.343
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
Nuclear hormone receptor RXR


Mass: 24697.746 Da / Num. of mol.: 4 / Fragment: UNP residues 266-484, Ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8MX78
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M Na acetate, 0.1 M ADA pH=6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorDetector: CCD / Date: May 1, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.79→15 Å / Num. all: 22831 / Num. obs: 22831 / % possible obs: 90.34 % / Observed criterion σ(F): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 5.4
Reflection shellResolution: 2.79→2.89 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.2 / % possible all: 75

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LBD

1lbd
PDB Unreleased entry


Resolution: 2.79→15 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 1167 random
Rwork0.202 --
all0.202 22811 -
obs0.202 22811 -
Displacement parametersBiso mean: 56.5 Å2
Refinement stepCycle: LAST / Resolution: 2.79→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6147 0 0 49 6196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_other_d0.016
X-RAY DIFFRACTIONr_angle_other_deg1.67
LS refinement shellResolution: 2.79→2.86 Å / Num. reflection obs: 1339

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