+Open data
-Basic information
Entry | Database: PDB / ID: 1rfx | ||||||
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Title | Crystal Structure of resisitin | ||||||
Components | Resistin | ||||||
Keywords | HORMONE/GROWTH FACTOR / HORMONE / GLUCOSE UPTAKE / RESISTIN/FIZZ FAMILY / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of collagen metabolic process / positive regulation of progesterone secretion / negative regulation of feeding behavior / positive regulation of smooth muscle cell migration / fat cell differentiation / positive regulation of synaptic transmission / Neutrophil degranulation / positive regulation of smooth muscle cell proliferation / response to insulin / hormone activity ...positive regulation of collagen metabolic process / positive regulation of progesterone secretion / negative regulation of feeding behavior / positive regulation of smooth muscle cell migration / fat cell differentiation / positive regulation of synaptic transmission / Neutrophil degranulation / positive regulation of smooth muscle cell proliferation / response to insulin / hormone activity / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å | ||||||
Authors | Patel, S.D. / Rajala, M.W. / Scherer, P.E. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Science / Year: 2004 Title: Disulfide-dependent multimeric assembly of resistin family hormones Authors: Patel, S.D. / Rajala, M.W. / Rossetti, L. / Scherer, P.E. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rfx.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rfx.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rfx_validation.pdf.gz | 479.3 KB | Display | wwPDB validaton report |
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Full document | 1rfx_full_validation.pdf.gz | 485.1 KB | Display | |
Data in XML | 1rfx_validation.xml.gz | 16 KB | Display | |
Data in CIF | 1rfx_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rfx ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rfx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 10182.790 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: RETN / Plasmid: pFM1 / Production host: Homo sapiens (human) / References: UniProt: Q99P87 |
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-Non-polymers , 5 types, 225 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 2 Details: 0.1M Sodium acetate, 8% PEG 4000, 0.1M Potassium Chloride, pH 2., VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.54975 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54975 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 24119 / Num. obs: 24119 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 25.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 9.6 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.002→14.86 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.109 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.002→14.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.053 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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