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- PDB-2q60: Crystal structure of the ligand binding domain of polyandrocarpa ... -

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Basic information

Entry
Database: PDB / ID: 2q60
TitleCrystal structure of the ligand binding domain of polyandrocarpa misakiensis rxr in tetramer in absence of ligand
ComponentsRetinoid X receptor
KeywordsTRANSCRIPTION / Nuclear receptor. RXR ligand binding domain / Apo-tetramer
Function / homology
Function and homology information


nuclear steroid receptor activity / sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus
Similarity search - Function
Retinoid X receptor/HNF4 / 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/HNF4 / 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
Biological speciesPolyandrocarpa misakiensis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBorel, F. / De Groot, A. / Juillan-Binard, C. / De Rosny, E. / Laudet, V. / Pebay-Peyroula, E. / Fontecilla-Camps, J.-C. / Ferrer, J.-L.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the ligand-binding domain of the retinoid X receptor from the ascidian polyandrocarpa misakiensis.
Authors: Borel, F. / de Groot, A. / Juillan-Binard, C. / de Rosny, E. / Laudet, V. / Pebay-Peyroula, E. / Fontecilla-Camps, J.C. / Ferrer, J.L.
History
DepositionJun 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 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: Retinoid X receptor
B: Retinoid X receptor
C: Retinoid X receptor
D: Retinoid X receptor


Theoretical massNumber of molelcules
Total (without water)116,2704
Polymers116,2704
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.260, 96.120, 151.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer

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Components

#1: Protein
Retinoid X receptor


Mass: 29067.512 Da / Num. of mol.: 4 / Fragment: ligand binding domain / Mutation: I247V,L257P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polyandrocarpa misakiensis (invertebrata)
Gene: PmRXR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9UAF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Pipes. 17% Peg 4K. 15mM Sodium chloride. 1mM n-dodecyl B-D-maltoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→48.224 Å / Num. all: 27360 / Num. obs: 27210 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.26 % / Biso Wilson estimate: 55.294 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.51
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.22 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 13392 / Num. unique all: 2560 / % possible all: 98.6

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Phasing

Phasing MRRfactor: 0.553 / Cor.coef. Fo:Fc: 0.384
Highest resolutionLowest resolution
Rotation3 Å48.22 Å
Translation3 Å48.22 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RXR part of PDB ENTRY 1XDK

1xdk


Resolution: 2.9→48.22 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.796 / SU B: 46.865 / SU ML: 0.397 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.192 / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.325 1361 5 %RANDOM
Rwork0.269 ---
obs0.272 27207 100 %-
all-27210 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.075 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å20 Å20 Å2
2--4.66 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 0 0 175 6256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216209
X-RAY DIFFRACTIONr_bond_other_d0.0010.025778
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9758408
X-RAY DIFFRACTIONr_angle_other_deg0.762313336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7823.164256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.518151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8251546
X-RAY DIFFRACTIONr_chiral_restr0.0560.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
X-RAY DIFFRACTIONr_nbd_refined0.1870.21782
X-RAY DIFFRACTIONr_nbd_other0.1620.26424
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23108
X-RAY DIFFRACTIONr_nbtor_other0.080.23528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0620.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1060.219
X-RAY DIFFRACTIONr_mcbond_it0.2911.54059
X-RAY DIFFRACTIONr_mcbond_other0.021.51589
X-RAY DIFFRACTIONr_mcangle_it0.53226328
X-RAY DIFFRACTIONr_scbond_it0.232382
X-RAY DIFFRACTIONr_scangle_it0.344.52080
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 97 -
Rwork0.348 1850 -
obs-1947 100 %
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)
13.078-0.55474.45072.4651-1.83636.88770.1430.6389-0.3346-0.0586-0.3925-0.6557-0.11830.87380.2494-0.28240.12150.01530.32370.0881-0.048557.39542.517242.8764
21.3989-0.27211.06160.4268-0.62731.2793-0.04580.1627-0.00660.0001-0.05550.131-0.19480.36960.1013-0.0069-0.0422-0.0422-0.0160.0247-0.005942.46169.929838.5384
33.1392-2.08411.90971.4956-0.79033.19760.05280.5715-0.04590.82520.2471-0.27780.17380.0063-0.29990.0138-0.0033-0.00870.20350.0797-0.243129.12214.502769.7
41.23750.03331.23990.01170.00371.54750.0874-0.5157-0.0973-0.0989-0.00030.00340.0154-0.2871-0.0872-0.0552-0.0212-0.00130.0890.047-0.052225.423.31654.8077
50.0418-0.1047-0.42810.26211.0724.3842-0.15450.1461-0.18260.10030.07870.0079-0.30420.24020.07580.0113-0.0601-0.0340.1850.0083-0.156112.93316.9077-0.3906
61.83740.20641.19890.11490.33871.23640.02120.3734-0.08470.09940.025-0.00960.00960.1454-0.0462-0.0241-0.0122-0.0081-0.0143-0.0145-0.031216.74624.63214.4308
79.6262-3.7004-2.64485.5486.01496.7821-0.197-0.3464-0.63690.3983-0.12350.90480.4234-1.09160.32050.0062-0.0393-0.00350.12490.0661-0.121-15.35541.840126.3622
82.8716-0.02641.59830.2724-0.03130.9613-0.1031-0.61840.0232-0.09510.0483-0.0961-0.2316-0.56180.0548-0.05710.0579-0.0420.0506-0.0079-0.0108-0.84519.384230.5499
90.60940.16350.35620.04990.04560.6216-0.00820.0322-0.00670.054-0.01820.0101-0.0104-0.01940.0263-0.00160.0334-0.0301-0.103-0.00670.041321.13666.20633.2952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A103 - 120
2X-RAY DIFFRACTION2A145 - 324
3X-RAY DIFFRACTION3B106 - 121
4X-RAY DIFFRACTION4B144 - 325
5X-RAY DIFFRACTION5C105 - 122
6X-RAY DIFFRACTION6C142 - 326
7X-RAY DIFFRACTION7D103 - 121
8X-RAY DIFFRACTION8D146 - 323
9X-RAY DIFFRACTION9A339 - 387
10X-RAY DIFFRACTION9C339 - 385
11X-RAY DIFFRACTION9B339 - 380
12X-RAY DIFFRACTION9D339 - 375

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