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- PDB-3ry9: Crystal Structure of the Resurrected Ancestral Glucocorticoid Rec... -

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Basic information

Entry
Database: PDB / ID: 3ry9
TitleCrystal Structure of the Resurrected Ancestral Glucocorticoid Receptor 1 in complex with DOC
ComponentsAncestral Glucocorticoid Receptor 1
KeywordsSTEROID BINDING PROTEIN / resurrected protein / steroid receptor / nuclear receptor / common ancestor / evolution
Function / homologyRetinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / DESOXYCORTICOSTERONE
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOrtlund, E.A.
CitationJournal: PLoS Genet / Year: 2011
Title: Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor.
Authors: Carroll, S.M. / Ortlund, E.A. / Thornton, J.W.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Ancestral Glucocorticoid Receptor 1
B: Ancestral Glucocorticoid Receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4637
Polymers57,5952
Non-polymers8685
Water4,306239
1
A: Ancestral Glucocorticoid Receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2203
Polymers28,7981
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ancestral Glucocorticoid Receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2434
Polymers28,7981
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.421, 49.144, 100.369
Angle α, β, γ (deg.)90.00, 105.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ancestral Glucocorticoid Receptor 1 / AncGR1


Mass: 28797.551 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Gene: resurrected gene / Plasmid: pLIC_MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-1CA / DESOXYCORTICOSTERONE / 4-PREGNEN-21-OL-3,20-DIONE / DOC / 21-HYDROXYPROGESTERONE / 11-Deoxycorticosterone


Mass: 330.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O3 / Comment: hormone*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5-2.8 M sodium acetate trihydrate, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→96.674 Å / Num. all: 48182 / Num. obs: 48012 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 29.488 Å2 / Rsym value: 0.048 / Net I/σ(I): 13
Reflection shellResolution: 1.95→2 Å / % possible all: 78.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q3Y

2q3y


Resolution: 1.95→96.67 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.21607 2432 RANDOM
Rwork0.18123 --
all0.183 45580 -
obs-45420 -
Displacement parametersBiso max: 105.4 Å2 / Biso mean: 29.4878 Å2 / Biso min: 12.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.132 Å0.284 Å
Refinement stepCycle: LAST / Resolution: 1.95→96.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 61 239 4263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_angle_refined_deg1.093

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