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Open data
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Basic information
Entry | Database: PDB / ID: 1e5l | ||||||
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Title | Apo saccharopine reductase from Magnaporthe grisea | ||||||
![]() | SACCHAROPINE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / SACCHAROPINE REDUCTASE / LYSINE BIOSYNTHESIS / ALPHA- AMINOADIPATE PATHWAY | ||||||
Function / homology | ![]() saccharopine dehydrogenase (NADP+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity / lysine biosynthetic process via aminoadipic acid / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G. | ||||||
![]() | ![]() Title: Crystal Structure of Saccharopine Reductase from Magnaporthe Grisea, an Enzyme of the Alpha-Aminoadipate Pathway of Lysine Biosynthesis Authors: Johansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Cloning, Expression, Purification and Crystallization of Saccharopine Reductase from Magnaporthe Grisea, an Enzyme of the Alpha-Aminoadipate Pathway of Lysine Biosynthesis Authors: Johansson, E. / Steffens, J.J. / Emptage, M. / Lindqvist, Y. / Schneider, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.7 KB | Display | ![]() |
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PDB format | ![]() | 145.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.9 KB | Display | ![]() |
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Full document | ![]() | 466.3 KB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e5qC ![]() 1ff9SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.56243, 0.35127, 0.74852), Vector: |
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Components
#1: Protein | Mass: 49156.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9P4R4*PLUS, saccharopine dehydrogenase (NADP+, L-glutamate-forming) #2: Water | ChemComp-HOH / | Sequence details | DESCRIBED IN JOHANSSON ET AL.(2000) ACTA CRYST. D56 662-664 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4 Details: 8 MG/ML PROTEIN, 11-14 % (W/W) PEG6000, 0.1 M CITRIC ACID PH 4.0, 0.1 % BETA-OCTYLGLUCOSIDE, 1 MM DTT | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.104 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 40017 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.3 / % possible all: 82.2 |
Reflection | *PLUS Num. measured all: 386685 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 82.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FF9 Resolution: 2.4→19.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2970901.79 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES Details: MLF REFINEMENT TARGET
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Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.274 |