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- PDB-2q1v: Ancestral corticoid receptor in complex with cortisol -

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Basic information

Entry
Database: PDB / ID: 2q1v
TitleAncestral corticoid receptor in complex with cortisol
ComponentsAncCR
KeywordsTRANSCRIPTION / Nuclear Receptor / cortisol / corticoid / evolution / common ancestor / mineralocorticoid
Function / homologyRetinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOrtlund, E.A. / Redinbo, M.R.
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 25, 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 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AncCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5033
Polymers29,0531
Non-polymers4512
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.873, 79.873, 114.588
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 AncCR


Mass: 29052.707 Da / Num. of mol.: 1 / Mutation: C71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pMALCH10T_AncCRLBD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PlysS
#2: Chemical ChemComp-PDN / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE / PREDNISONE / 1,4 PREGNADIENE-17ALPHA,21-DIOL-3,11,20-TRIONE / 1-CORTISONE / DEHYDROCORTISONE


Mass: 358.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 9.5-15% PEG 3350, 5% glycerol, 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 27636 / Num. obs: 27603 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.089 / Net I/σ(I): 18.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 2702 / Rsym value: 0.375 / % possible all: 99.7

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Processing

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

Resolution: 1.95→46.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 121951.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1889 7 %RANDOM
Rwork0.207 ---
obs0.207 27176 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8628 Å2 / ksol: 0.375778 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.95→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 32 181 2199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 281 6.8 %
Rwork0.267 3840 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.pargol.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5COR.par

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