+Open data
-Basic information
Entry | Database: PDB / ID: 2izz | ||||||
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Title | Crystal structure of human pyrroline-5-carboxylate reductase | ||||||
Components | PYRROLINE-5-CARBOXYLATE REDUCTASE 1 | ||||||
Keywords | OXIDOREDUCTASE / AMINO-ACID BIOSYNTHESIS / NADP / PROLINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / proline biosynthetic process / L-proline biosynthetic process / Glutamate and glutamine metabolism / 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: 1.95 Å | ||||||
Authors | Pike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. ...Pike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Pyrroline-5-Carboxylate Reductase Authors: Pike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. ...Authors: Pike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2izz.cif.gz | 277.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2izz.ent.gz | 224.3 KB | Display | PDB format |
PDBx/mmJSON format | 2izz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/2izz ftp://data.pdbj.org/pub/pdb/validation_reports/iz/2izz | HTTPS FTP |
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-Related structure data
Related structure data | 2ag8S 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34043.156 Da / Num. of mol.: 5 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P32322, pyrroline-5-carboxylate reductase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-EDO / #4: 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: 2.43 Å3/Da / Density % sol: 49.5 % |
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Crystal grow | pH: 7.5 Details: 20% PEG3350, 10% ETHYLENE GLYCOL 0.2M NA2SO4, 0.1M BIS-TRIS PROPANE PH7.5, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.976 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 117744 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AG8 Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.176 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.114 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→40 Å
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Refine LS restraints |
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