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- PDB-7raf: AncAR1-Rev - progesterone - Tif2 -

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Basic information

Entry
Database: PDB / ID: 7raf
TitleAncAR1-Rev - progesterone - Tif2
Components
  • Ancestral androgen receptor
  • Transcriptional mediator/intermediary factor 2
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / evolution / ancestral gene resurrection / nuclear receptor / transcription / SIGNALING PROTEIN / SIGNALING PROTEIN-TRANSCRIPTION complex
Function / homologyRetinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / PROGESTERONE
Function and homology information
Biological speciesEscherichia phage EcSzw-2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsColucci, J.K.
CitationJournal: To Be Published
Title: AncAR1-Rev - progesterone - Tif2
Authors: Colucci, J.K.
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)31,3176
Polymers30,7272
Non-polymers5914
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-6 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.099, 69.099, 145.258
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-Rev


Mass: 29262.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage EcSzw-2 (virus) / Production host: Escherichia phage EcSzw-2 (virus)
#2: Protein/peptide Transcriptional mediator/intermediary factor 2 / TIF2


Mass: 1464.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia phage EcSzw-2 (virus)
#3: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2 / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: 25% PEG8000 and 50mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→33.7 Å / Num. obs: 51730 / % possible obs: 99.8 % / Redundancy: 31.6 % / Rsym value: 0.109 / Net I/σ(I): 31.6
Reflection shellResolution: 1.5→10 Å / Num. unique obs: 51730 / Rsym value: 0.437

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMACv1.0refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AMA

2ama


Resolution: 1.551→33.612 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1688 2000 3.87 %
Rwork0.1529 --
obs0.1536 51728 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.13 Å2 / Biso mean: 25.7449 Å2 / Biso min: 9.71 Å2
Refinement stepCycle: final / Resolution: 1.551→33.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 94 242 2461
Biso mean--31.27 38.67 -
Num. residues----258
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.81422.8614-5.9037.2968-4.81449.6689-0.06750.4545-0.1377-0.3130.1406-0.5857-0.26150.3440.00860.1421-0.05820.0050.2323-0.05140.20314.8418-23.1739.9337
21.52630.3672-0.08361.88280.2571.26120.0507-0.1226-0.10420.0839-0.0331-0.0530.0880.0648-0.01590.08970.011-0.01960.13590.00870.1179-1.8997-29.888319.4653
31.7546-0.0108-0.34041.1927-0.66414.8941-0.00550.1115-0.2554-0.086200.0630.2755-0.17260.01350.157-0.0184-0.02610.1117-0.04090.1485-9.4864-38.8478.3862
44.6745-1.8568-2.17587.93044.11827.1075-0.01910.2169-0.1185-0.13850.1118-0.27950.08160.2285-0.09540.0577-0.0258-0.0130.146-0.01340.1034.8183-25.65656.6322
54.3782-1.099-1.95814.49361.46514.3837-0.07760.26120.225-0.24630.093-0.194-0.13450.092-0.05680.1023-0.0153-0.02640.14580.0230.11894.5366-13.44648.0101
66.12890.9589-4.8851.5169-1.09926.69820.05440.43550.1051-0.25550.0310.0949-0.1546-0.0682-0.1480.1395-0.0043-0.04520.16-0.0120.1113-7.8555-23.57075.878
73.76020.90011.81053.56440.35811.58990.1117-0.2963-0.03330.3712-0.1340.0570.0141-0.10150.01890.10910.01490.03280.1797-0.01130.1083-14.5387-26.000926.0188
82.6221-1.27761.20143.48261.81692.80710.58890.70990.59-0.5015-0.0076-0.2291-0.4171-0.1058-0.50010.20480.04260.02160.28560.02010.2242-9.2056-13.36598.4631
97.45681.71750.23346.1166-1.28416.85070.0061-0.12990.03490.2588-0.0635-0.5126-0.12850.74140.04470.1651-0.0101-0.03860.2479-0.01220.12853.6013-20.494431.2012
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 907 )A883 - 907
8X-RAY DIFFRACTION8chain 'A' and (resid 908 through 917 )A908 - 917
9X-RAY DIFFRACTION9chain 'D' and (resid 743 through 753 )D743 - 753

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