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- PDB-4xld: Crystal structure of the human PPARg-LBD/rosiglitazone complex ob... -

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Basic information

Entry
Database: PDB / ID: 4xld
TitleCrystal structure of the human PPARg-LBD/rosiglitazone complex obtained by dry co-crystallization and in situ diffraction
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsGENE REGULATION / nuclear receptor ligand screening
Function / homology
Function and homology information


Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane ...Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane / aerobic respiration / mitochondrial inner membrane / mitochondrion / nucleoplasm
Similarity search - Function
NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / Retinoid X Receptor / Retinoid X Receptor / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-BRL / FORMIC ACID / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDelfosse, V. / Guichou, J.-F.
Funding support France, 1items
OrganizationGrant numberCountry
FRISBIANR-10-INSB-05-01 France
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography.
Authors: Gelin, M. / Delfosse, V. / Allemand, F. / Hoh, F. / Sallaz-Damaz, Y. / Pirocchi, M. / Bourguet, W. / Ferrer, J.L. / Labesse, G. / Guichou, J.F.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1563
Polymers33,7521
Non-polymers4032
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-6 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.990, 66.990, 157.440
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 Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 33752.066 Da / Num. of mol.: 1 / Fragment: UNP residues 203-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37231
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-BRL / 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) / BRL49653 / ROSIGLITAZONE


Mass: 357.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 3-4 M Sodium Formate / PH range: 7-7.5

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Data collection

DiffractionMean temperature: 291 K
Ambient temp details: in situ (in plate), at room temperature
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.45→47.37 Å / Num. obs: 12488 / % possible obs: 90 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.154 / Net I/σ(I): 7.43
Reflection shellResolution: 2.45→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4.68 / % possible all: 77.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(phenix.refine: 1.8.4_1496)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2prg

2prg


Resolution: 2.45→47.369 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 937 7.51 %Random selection
Rwork0.1913 ---
obs0.1936 12485 89.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.7 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 28 25 2096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042118
X-RAY DIFFRACTIONf_angle_d0.7992869
X-RAY DIFFRACTIONf_dihedral_angle_d15.294782
X-RAY DIFFRACTIONf_chiral_restr0.029336
X-RAY DIFFRACTIONf_plane_restr0.004369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4502-2.57940.2831120.26451377X-RAY DIFFRACTION77
2.5794-2.7410.3181330.251648X-RAY DIFFRACTION93
2.741-2.95260.2691360.23411672X-RAY DIFFRACTION93
2.9526-3.24970.24481370.22481690X-RAY DIFFRACTION93
3.2497-3.71980.21951370.1741697X-RAY DIFFRACTION93
3.7198-4.68580.16681390.15291703X-RAY DIFFRACTION92
4.6858-47.37790.21331430.18071761X-RAY DIFFRACTION89

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