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- PDB-2q3y: Ancestral Corticiod Receptor in Complex with DOC -

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Basic information

Entry
Database: PDB / ID: 2q3y
TitleAncestral Corticiod Receptor in Complex with DOC
Components
  • Ancestral Corticiod Receptor
  • Nuclear receptor 0B2
KeywordsTRANSCRIPTION / Nuclear Receptor / mineralocoticiod / Ligand Binding Domain / DOC / cortisol / evolution
Function / homology
Function and homology information


bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / cholesterol metabolic process / circadian regulation of gene expression ...bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / cholesterol metabolic process / circadian regulation of gene expression / positive regulation of insulin secretion / response to organic cyclic compound / negative regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / circadian rhythm / transcription corepressor activity / response to ethanol / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of gene expression / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DESOXYCORTICOSTERONE / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOrtlund, E.A. / Bridgham, J.T. / Redinbo, M.R. / Thornton, J.W.
CitationJournal: Science / Year: 2007
Title: Crystal structure of an ancient protein: evolution by conformational epistasis
Authors: Ortlund, E.A. / Bridgham, J.T. / Redinbo, M.R. / Thornton, J.W.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999Sequence No suitable database reference was found for Chain A at time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral Corticiod Receptor
B: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4064
Polymers29,9842
Non-polymers4232
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.995, 78.995, 112.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ancestral Corticiod Receptor


Mass: 28936.465 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain / Mutation: C71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: PMALCH10T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 plysS
#2: Protein/peptide Nuclear receptor 0B2 / Orphan nuclear receptor SHP / Small heterodimer partner


Mass: 1047.246 Da / Num. of mol.: 1 / Fragment: hSHP NR Box1 / Source method: obtained synthetically / References: UniProt: Q15466
#3: Chemical ChemComp-1CA / DESOXYCORTICOSTERONE / 4-PREGNEN-21-OL-3,20-DIONE / DOC / 21-HYDROXYPROGESTERONE


Mass: 330.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O3 / 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.: 101 / 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: 2.92 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 14543 / Num. obs: 14500 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.58
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 10 / Num. unique all: 1404 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AncCR

Resolution: 2.4→37.27 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 118702.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 980 7 %RANDOM
Rwork0.196 ---
obs0.196 14036 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0596 Å2 / ksol: 0.342134 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.09 Å20 Å20 Å2
2---6.09 Å20 Å2
3---12.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 30 101 2196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 161 7.4 %
Rwork0.241 2028 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.pargol.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4DOC.parDOC.top
X-RAY DIFFRACTION5ion.paramwater.top

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