+Open data
-Basic information
Entry | Database: PDB / ID: 6lhm | ||||||
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Title | Structure of human PYCR2 | ||||||
Components | Pyrroline-5-carboxylate reductase 2 | ||||||
Keywords | OXIDOREDUCTASE / PYCR2 / carboxylate / P5CR / decamer / pentamer / Pyrroline-5-carboxylate reductase | ||||||
Function / homology | Function and homology information glutamine family amino acid metabolic process / pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process / cellular response to oxidative stress / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Baburajendran, N. | ||||||
Citation | Journal: Neuron / Year: 2020 Title: Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2. Authors: Escande-Beillard, N. / Loh, A. / Saleem, S.N. / Kanata, K. / Hashimoto, Y. / Altunoglu, U. / Metoska, A. / Grandjean, J. / Ng, F.M. / Pomp, O. / Baburajendran, N. / Wong, J. / Hill, J. / ...Authors: Escande-Beillard, N. / Loh, A. / Saleem, S.N. / Kanata, K. / Hashimoto, Y. / Altunoglu, U. / Metoska, A. / Grandjean, J. / Ng, F.M. / Pomp, O. / Baburajendran, N. / Wong, J. / Hill, J. / Beillard, E. / Cozzone, P. / Zaki, M. / Kayserili, H. / Hamada, H. / Shiratori, H. / Reversade, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lhm.cif.gz | 465.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lhm.ent.gz | 385 KB | Display | PDB format |
PDBx/mmJSON format | 6lhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lhm_validation.pdf.gz | 473.7 KB | Display | wwPDB validaton report |
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Full document | 6lhm_full_validation.pdf.gz | 499.2 KB | Display | |
Data in XML | 6lhm_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 6lhm_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/6lhm ftp://data.pdbj.org/pub/pdb/validation_reports/lh/6lhm | HTTPS FTP |
-Related structure data
Related structure data | 2izzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 31737.818 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR2 / Production host: Escherichia coli (E. coli) References: UniProt: Q96C36, pyrroline-5-carboxylate reductase |
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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: 2.75 Å3/Da / Density % sol: 55.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Carboxylic acids, 0.1M Buffer system 3 pH 8.5, 50% v/v Precipitant Mix 3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→46.904 Å / Num. obs: 24754 / % possible obs: 97.68 % / Redundancy: 8.2 % / CC1/2: 0.829 / Net I/σ(I): 8.75 |
Reflection shell | Resolution: 3.4→3.522 Å / Num. unique obs: 20319 / CC1/2: 0.659 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IZZ Resolution: 3.4→46.904 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.4 Å2 / Biso mean: 76.6374 Å2 / Biso min: 33.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→46.904 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -7.2772 Å / Origin y: 26.959 Å / Origin z: -20.3521 Å
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Refinement TLS group |
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