+Open data
-Basic information
Entry | Database: PDB / ID: 2vv4 | ||||||
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Title | hPPARgamma Ligand binding domain in complex with 6-oxoOTE | ||||||
Components | (PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA) x 2 | ||||||
Keywords | RECEPTOR / NUCLEAR RECEPTOR / LIGAND BINDING DOMAIN / OXIDISED FATTY ACID / TRANSCRIPTION FACTOR | ||||||
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 | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Itoh, T. / Fairall, L. / Schwabe, J.W.R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural Basis for the Activation of Pparg by Oxidised Fatty Acids Authors: Itoh, T. / Fairall, L. / Amin, K. / Inaba, Y. / Szanto, A. / Balint, B.L. / Nagy, L. / Yamamoto, K. / Schwabe, J.W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vv4.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vv4.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vv4_validation.pdf.gz | 892.4 KB | Display | wwPDB validaton report |
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Full document | 2vv4_full_validation.pdf.gz | 904.2 KB | Display | |
Data in XML | 2vv4_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 2vv4_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vv4 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vv4 | HTTPS FTP |
-Related structure data
Related structure data | 2vsrC 2vstC 2vv0C 2vv1C 2vv2C 2vv3C 2i4pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31449.520 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475 Source method: isolated from a genetically manipulated source Details: 6-OXOOTE / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P37231 |
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#2: Protein | Mass: 31463.547 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475 Source method: isolated from a genetically manipulated source Details: 6-OXOOTE / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P37231 |
#3: Chemical | ChemComp-6OC / ( |
#4: Chemical | ChemComp-6OB / ( |
#5: Water | ChemComp-HOH / |
Nonpolymer details | 6-OXOOCTADECATRIENOIC ACID (6OC): LIGAND IS COVALENTLY COUPLED AT C8 TO CYS285 IN MONOMER A 6- ...6-OXOOCTADEC |
Sequence details | RESIDUE NUMBERING CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.5 % / Description: NONE |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8 Details: PH 8, TRIS 100MM, 0.7M NACITRATE, 1MM TCEP, 0.5MM EDTA, VAPOUR DIFFUSION, DARK, UNDER NITROGEN, 22 DEGREES CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→51.03 Å / Num. obs: 53512 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I4P Resolution: 2.35→51.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1765036.14 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5652 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→51.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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