+Open data
-Basic information
Entry | Database: PDB / ID: 5uat | ||||||
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Title | Structure of human PYCR-1 complexed with NADPH | ||||||
Components | Pyrroline-5-carboxylate reductase 1, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / AMINO-ACID BIOSYNTHESIS / PROLINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Tanner, J.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1. Authors: Christensen, E.M. / Patel, S.M. / Korasick, D.A. / Campbell, A.C. / Krause, K.L. / Becker, D.F. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uat.cif.gz | 512.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uat.ent.gz | 420.2 KB | Display | PDB format |
PDBx/mmJSON format | 5uat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uat_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5uat_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5uat_validation.xml.gz | 52.6 KB | Display | |
Data in CIF | 5uat_validation.cif.gz | 75.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/5uat ftp://data.pdbj.org/pub/pdb/validation_reports/ua/5uat | HTTPS FTP |
-Related structure data
Related structure data | 5uauC 5uavC 5uawC 5uaxC 2izzS 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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3 |
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4 |
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Unit cell |
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Details | The authors state that based on analytical ultracentrifugation sedimentation velocity experiments, the protein is primarily a decamer at 6 mg/mL (180 micro molar based on monomer molecular weight). Lower molecular weight species are also observed at a protein concentration of 0.8 mg/mL. |
-Components
#1: Protein | Mass: 34043.156 Da / Num. of mol.: 5 / Fragment: residues 1-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR1 / Production host: Escherichia coli (E. coli) References: UniProt: P32322, pyrroline-5-carboxylate reductase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: 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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 300 mM Na2SO4, 16-18% (w/v) polyethylene glycol (PEG) 3350, and 0.1 M HEPES at pH 7.5. The crystal was soaked in the cryobuffer containing 100 mM NADPH |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 18, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.92→64.24 Å / Num. obs: 126545 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Net I/σ(I): 14.9 / Num. measured all: 879308 / Scaling rejects: 80 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IZZ Resolution: 1.92→64.235 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.8 Å2 / Biso mean: 32.3083 Å2 / Biso min: 10.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→64.235 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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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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