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- PDB-1ilh: Crystal Structure of Human Pregnane X Receptor Ligand Binding Dom... -

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Basic information

Entry
Database: PDB / ID: 1ilh
TitleCrystal Structure of Human Pregnane X Receptor Ligand Binding Domain Bound to SR12813
ComponentsORPHAN NUCLEAR RECEPTOR PXR
KeywordsGENE REGULATION / nuclear receptor / multiple binding modes / xenobiotic / promiscuous / ligand
Function / homology
Function and homology information


intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / 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 / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SRL / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsWatkins, R.E. / Redinbo, M.R.
CitationJournal: Science / Year: 2001
Title: The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity.
Authors: Watkins, R.E. / Wisely, G.B. / Moore, L.B. / Collins, J.L. / Lambert, M.H. / Williams, S.P. / Willson, T.M. / Kliewer, S.A. / Redinbo, M.R.
History
DepositionMay 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: ORPHAN NUCLEAR RECEPTOR PXR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7852
Polymers36,2811
Non-polymers5051
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.345, 91.345, 85.302
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 ORPHAN NUCLEAR RECEPTOR PXR / PREGNANE X RECEPTOR


Mass: 36280.867 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PXR / Plasmid: pRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75469
#2: Chemical ChemComp-SRL / [2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC ACID DIETHLYL ESTER / SR12813


Mass: 504.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H42O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: isopropanol, imidazole, glycerol, sodium chloride, Tris-HCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1250 mM1dropNaCl
220 mMTris-HCl1drop
35 %(v/v)glycerol1drop
45 mMdithiothreitol1drop
52.5 mMEDTA1drop
65 mg/mlprotein1drop
750 mMimidazole1reservoir
810 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000 / Details: mirrors
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: 2.76→19.86 Å / Num. all: 133315 / Num. obs: 133315 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 25.9
Reflection shellResolution: 2.75→2.92 Å / Redundancy: 14 % / Rmerge(I) obs: 0.4 / % possible all: 89.8
Reflection
*PLUS
Num. obs: 9512
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DB1

1db1


Resolution: 2.76→19.86 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2779068.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 997 10.3 %RANDOM
Rwork0.222 ---
all-133315 --
obs-133315 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.16 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.13 Å20 Å20 Å2
2--4.13 Å20 Å2
3----8.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.76→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 99 166 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it10.182
X-RAY DIFFRACTIONc_scangle_it11.452.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 132 9.1 %
Rwork0.277 1318 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SR12813.PARAMSR12813.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / % reflection Rfree: 9.1 % / Rfactor Rwork: 0.277

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