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- PDB-4ltw: Ancestral Ketosteroid Receptor-Progesterone-Mifepristone Complex -

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Basic information

Entry
Database: PDB / ID: 4ltw
TitleAncestral Ketosteroid Receptor-Progesterone-Mifepristone Complex
ComponentsAncestral Steroid Receptor 2
KeywordsHORMONE RECEPTOR / Nuclear Receptor / Steroid Receptor
Function / homologyRetinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / Chem-486 / PROGESTERONE
Function and homology information
Biological speciesAncestral Gene
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.045 Å
AuthorsOrtlund, E.A. / Colucci, J.K.
CitationJournal: Plos One / Year: 2013
Title: X-ray crystal structure of the ancestral 3-ketosteroid receptor-progesterone-mifepristone complex shows mifepristone bound at the coactivator binding interface.
Authors: Colucci, J.K. / Ortlund, E.A.
History
DepositionJul 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

Downloads & links

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Assembly

Deposited unit
A: Ancestral Steroid Receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4737
Polymers29,0151
Non-polymers1,4586
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.920, 74.950, 95.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ancestral Steroid Receptor 2


Mass: 29014.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancestral Gene / Plasmid: LIC-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#3: Chemical ChemComp-486 / 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE / RU-486 / MIFEPRISTONE


Mass: 429.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H35NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.8 M MgSO4, 10 % glycerol, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→43.8 Å / Num. all: 25187 / Num. obs: 25036 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.05-2.1194
2.1-2.15198
2.15-2.22199
2.22-2.29199
2.29-2.371100
2.37-2.461100
2.46-2.581100
2.58-2.71199
2.71-2.881100
2.88-3.11100
3.1-3.421100
3.42-3.911100
3.91-4.931100
4.93-43.81100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FN9

4fn9


Resolution: 2.045→43.77 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1993 7.98 %
Rwork0.1793 --
obs0.1819 24966 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.045→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 103 153 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132187
X-RAY DIFFRACTIONf_angle_d1.6632976
X-RAY DIFFRACTIONf_dihedral_angle_d17.31822
X-RAY DIFFRACTIONf_chiral_restr0.314325
X-RAY DIFFRACTIONf_plane_restr0.007371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0452-2.09630.31291330.25411523X-RAY DIFFRACTION94
2.0963-2.1530.26811410.22251613X-RAY DIFFRACTION98
2.153-2.21640.25321390.20391597X-RAY DIFFRACTION99
2.2164-2.28790.24441420.1891628X-RAY DIFFRACTION99
2.2879-2.36970.24221370.17131602X-RAY DIFFRACTION100
2.3697-2.46450.20381430.17281632X-RAY DIFFRACTION100
2.4645-2.57670.20551420.1681656X-RAY DIFFRACTION100
2.5767-2.71250.24331420.1691614X-RAY DIFFRACTION99
2.7125-2.88240.20631400.17951653X-RAY DIFFRACTION100
2.8824-3.10490.24011430.17881644X-RAY DIFFRACTION100
3.1049-3.41730.21631450.18681667X-RAY DIFFRACTION100
3.4173-3.91150.19441440.17231668X-RAY DIFFRACTION100
3.9115-4.9270.15781480.15171699X-RAY DIFFRACTION100
4.927-43.78010.21981540.18871777X-RAY DIFFRACTION100

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