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Yorodumi- PDB-1e5q: Ternary complex of saccharopine reductase from Magnaporthe grisea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e5q | ||||||
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Title | Ternary complex of saccharopine reductase from Magnaporthe grisea, NADPH and saccharopine | ||||||
Components | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | ||||||
Keywords | OXIDOREDUCTASE / SACCHAROPINE REDUCTASE / NADPH / LYSINE BIOSYNTHESIS / ALPHA- AMINOADIPATE PATHWAY | ||||||
Function / homology | Function and homology information 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 | Magnaporthe oryzae (rice blast fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Johansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G. | ||||||
Citation | Journal: Structure / Year: 2000 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e5q.cif.gz | 730 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e5q.ent.gz | 607.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e5q_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 1e5q_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 1e5q_validation.xml.gz | 157.1 KB | Display | |
Data in CIF | 1e5q_validation.cif.gz | 219.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/1e5q ftp://data.pdbj.org/pub/pdb/validation_reports/e5/1e5q | HTTPS FTP |
-Related structure data
Related structure data | 1e5lC 1ff9SC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 49156.262 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: LYS3, MGG_08564 / Plasmid: PDB45 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FM5/PDB45 References: UniProt: Q9P4R4, saccharopine dehydrogenase (NADP+, L-glutamate-forming) #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-SHR / #4: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.25 Details: 8 MG/ML PROTEIN, 1 MM SACCHAROPINE, 1 MM NADPH, 20 % (W/W) PEG8000, 0.1 M TRIS-HCL PH 7.25, 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8424 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 250975 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.5 / % possible all: 96.5 |
Reflection | *PLUS Num. measured all: 2072876 |
Reflection shell | *PLUS % possible obs: 96.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FF9 Resolution: 2.1→19.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3423402.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.4148 Å2 / ksol: 0.335216 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.006 / 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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