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- PDB-7rae: AncAR1 - progesterone - Tif2 -

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Basic information

Entry
Database: PDB / ID: 7rae
TitleAncAR1 - progesterone - Tif2
Components
  • Ancestral androgen receptor
  • Transcriptional mediator/intermediary factor 2
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / DHT / androgen / nuclear receptor / ancient protein / evolution / TRANSCRIPTION / SIGNALING PROTEIN-TRANSCRIPTION complex
Function / homologyRetinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / 5-ALPHA-DIHYDROTESTOSTERONE
Function and homology information
Biological speciesEscherichia coli BL21 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsOrtlund, E.A.
CitationJournal: To Be Published
Title: AncAR1 - DHT - Tif2
Authors: Ortlund, E.A.
History
DepositionJul 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ancestral androgen receptor
D: Transcriptional mediator/intermediary factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3764
Polymers30,9932
Non-polymers3832
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.871, 68.871, 147.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ancestral androgen receptor / AncAR1


Mass: 29528.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria) / Strain: BL21 / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Transcriptional mediator/intermediary factor 2 / Tif2


Mass: 1464.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: HANGING DROP VAPOR DIFFUSION - 20 PERCENT PEG 1000, MES pH 6.5

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Data collection

DiffractionMean temperature: 173.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→29.4 Å / Num. obs: 172781 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 30.56 Å2 / Rsym value: 0.109 / Net I/σ(I): 17.4
Reflection shellResolution: 2.05→2.18 Å / Rmerge(I) obs: 0.437 / Num. unique obs: 21586 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PDBSETdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AMA
Resolution: 2.098→29.37 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 1076 5 %
Rwork0.1926 20426 -
obs0.1939 21502 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.97 Å2 / Biso mean: 38.8157 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 2.098→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 27 66 2225
Biso mean--27.66 41.95 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032230
X-RAY DIFFRACTIONf_angle_d0.5843023
X-RAY DIFFRACTIONf_chiral_restr0.039341
X-RAY DIFFRACTIONf_plane_restr0.004377
X-RAY DIFFRACTIONf_dihedral_angle_d2.3661863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.098-2.19340.26151290.2245246999
2.1934-2.30890.2611330.20832506100
2.3089-2.45350.21211320.19822512100
2.4535-2.64290.24771320.20192516100
2.6429-2.90860.22111330.1982531100
2.9086-3.3290.20481350.19562552100
3.329-4.19220.20321370.18292590100
4.1922-100.21231450.18392750100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.57310.8154-1.28635.507-6.36847.96240.01860.6172-0.324-0.3937-0.0377-0.63530.210.8815-0.14790.2371-0.0483-0.00340.6025-0.0860.524750.095810.52539.7795
22.92920.1462-0.70231.6944-0.51531.52650.0098-0.2163-0.17280.24090.0563-0.23270.14120.1195-0.07070.21960.0243-0.060.2561-0.00120.214933.33194.879518.8609
32.30050.44890.05722.047-0.34033.3189-0.07410.3794-0.5341-0.3320.07070.01660.3381-0.2881-0.0290.2621-0.016-0.0430.2571-0.0610.253525.4921-3.8267.573
42.11060.05-0.26242.96611.18263.4587-0.14710.2136-0.2165-0.24940.3986-0.46740.06610.5237-0.13230.2037-0.0238-0.00240.3951-0.05790.280340.03069.48886.1398
52.22690.76080.44292.9006-0.19212.0711-0.18660.51910.4859-0.24680.2897-0.2673-0.1620.2507-0.07050.2213-0.04090.01280.40260.0070.389939.792621.24397.0078
62.65020.8274-1.70881.9833-0.70953.66180.12170.51740.2857-0.16220.13980.1819-0.4469-0.0394-0.1510.2041-0.0123-0.0460.39320.00490.263627.158111.23815.8718
72.38680.21250.27442.8201-0.10361.41060.1015-0.2580.30730.42870.0980.2128-0.148-0.075-0.1390.24740.02020.0250.3119-0.02040.278122.041911.88321.1929
85.6732.6490.21715.6379-1.49236.82470.1722-0.28390.07070.46790.0942-0.1434-0.63530.0766-0.33690.4334-0.0765-0.08810.4825-0.0260.166137.243914.259631.1257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 670 through 680 )A670 - 680
2X-RAY DIFFRACTION2chain 'A' and (resid 681 through 757 )A681 - 757
3X-RAY DIFFRACTION3chain 'A' and (resid 758 through 797 )A758 - 797
4X-RAY DIFFRACTION4chain 'A' and (resid 798 through 813 )A798 - 813
5X-RAY DIFFRACTION5chain 'A' and (resid 814 through 848 )A814 - 848
6X-RAY DIFFRACTION6chain 'A' and (resid 849 through 882 )A849 - 882
7X-RAY DIFFRACTION7chain 'A' and (resid 883 through 917 )A883 - 917
8X-RAY DIFFRACTION8chain 'D' and (resid 743 through 751 )D743 - 751

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