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- PDB-2z4b: Estrogen receptor beta ligand-binding domain complexed to a benzo... -

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Basic information

Entry
Database: PDB / ID: 2z4b
TitleEstrogen receptor beta ligand-binding domain complexed to a benzopyran ligand
ComponentsEstrogen receptor beta
KeywordsTRANSCRIPTION / nuclear receptor ligand binding domain
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / 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) ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / 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
Chem-DC8 / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsWang, Y.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 3: Synthesis of cyclopentanone and cyclohexanone intermediates for C-ring modification.
Authors: Richardson, T.I. / Dodge, J.A. / Durst, G.L. / Pfeifer, L.A. / Shah, J. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Norman, B.H.
History
DepositionJun 14, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor beta
B: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0944
Polymers58,4572
Non-polymers6372
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-23 kcal/mol
Surface area18980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.523, 63.523, 250.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Estrogen receptor beta / ER-beta


Mass: 29228.648 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (Residues 251-505)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92731
#2: Chemical ChemComp-DC8 / (3AS,4R,9BR)-2,2-DIFLUORO-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL


Mass: 318.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16F2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris, pH 8.0, 2M sodium chloride, 4% PEG 6000, VAPOR DIFFUSION, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97943 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 24, 2005
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.34→33.28 Å / Num. all: 24017 / Num. obs: 23820 / % possible obs: 99.2 % / Observed criterion σ(I): 1.2 / Redundancy: 5.2 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 4.3
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 1.2 / Num. unique all: 3838 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2005refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→31.76 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1978978.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 868 3.6 %RANDOM
Rwork0.232 ---
obs-23820 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5159 Å2 / ksol: 0.365719 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å22.44 Å20 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.34→31.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 46 61 3595
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 2.34→2.49 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 125 3.2 %
Rwork0.3 3822 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION3water_rep.par
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5lig.par

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