+Open data
-Basic information
Entry | Database: PDB / ID: 5mlg | |||||||||
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Title | Crystal structure of rat prorenin | |||||||||
Components | Renin | |||||||||
Keywords | HYDROLASE / prorenin / rat | |||||||||
Function / homology | Function and homology information regulation of blood volume by renin-angiotensin / Metabolism of Angiotensinogen to Angiotensins / cellular response to xenobiotic stimulus => GO:0071466 / renin / response to xenobiotic stimulus => GO:0009410 / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade ...regulation of blood volume by renin-angiotensin / Metabolism of Angiotensinogen to Angiotensins / cellular response to xenobiotic stimulus => GO:0071466 / renin / response to xenobiotic stimulus => GO:0009410 / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / amyloid-beta metabolic process / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / kidney development / response to organic substance / regulation of blood pressure / male gonad development / apical part of cell / peptidase activity / endopeptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Yan, Y. / Read, R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Crystal structure of rat prorenin Authors: Yan, Y. / Zhou, A. / Read, R.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mlg.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mlg.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/5mlg ftp://data.pdbj.org/pub/pdb/validation_reports/ml/5mlg | HTTPS FTP |
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-Related structure data
Related structure data | 4amtS 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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Unit cell |
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-Components
#1: Protein | Mass: 42874.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ren1, Ren / Plasmid: pCEP4 / Cell (production host): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: P08424, renin |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.9M K/NaH2PO4, 0.1M HEPES PH7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50.4 Å / Num. obs: 23787 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.787 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AMT Resolution: 2.6→50.21 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.193 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.214 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.102 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→50.21 Å
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Refine LS restraints |
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