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Yorodumi- PDB-5u0k: C-terminal ankyrin repeats from human liver-type glutaminase (GAB/LGA) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u0k | ||||||
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Title | C-terminal ankyrin repeats from human liver-type glutaminase (GAB/LGA) | ||||||
Components | Glutaminase liver isoform, mitochondrial | ||||||
Keywords | HYDROLASE / Glutaminase / ankyrin / human / GLS2 | ||||||
Function / homology | Function and homology information glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / amino acid metabolic process / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / regulation of apoptotic process ...glutamine catabolic process / glutamate biosynthetic process / Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / amino acid metabolic process / reactive oxygen species metabolic process / TP53 Regulates Metabolic Genes / regulation of apoptotic process / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.548 Å | ||||||
Authors | Ferreira, I.M. / Pasquali, C.C. / Gonzalez, A. / Dias, S.M.G. / Ambrosio, A.L.B. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats. Authors: Pasquali, C.C. / Islam, Z. / Adamoski, D. / Ferreira, I.M. / Righeto, R.D. / Bettini, J. / Portugal, R.V. / Yue, W.W. / Gonzalez, A. / Dias, S.M.G. / Ambrosio, A.L.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u0k.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u0k.ent.gz | 161.1 KB | Display | PDB format |
PDBx/mmJSON format | 5u0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u0k_validation.pdf.gz | 513.1 KB | Display | wwPDB validaton report |
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Full document | 5u0k_full_validation.pdf.gz | 521.6 KB | Display | |
Data in XML | 5u0k_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 5u0k_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/5u0k ftp://data.pdbj.org/pub/pdb/validation_reports/u0/5u0k | HTTPS FTP |
-Related structure data
Related structure data | 5u0iSC 5u0jC 5uqeC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15840.733 Da / Num. of mol.: 10 / Fragment: UNP residues 485-602 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLS2, GA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9UI32, glutaminase #2: 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: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.1 M tri-sodium citrate, 0.1 M imidazole, 20 mM glutamine |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2015 / Details: Rh coated mirror | |||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.55→84.2 Å / Num. obs: 45005 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.1 | |||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U0I Resolution: 2.548→38.033 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.548→38.033 Å
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Refine LS restraints |
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LS refinement shell |
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