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Yorodumi- PDB-6t3e: Structure of Thermococcus litoralis Delta(1)-pyrroline-2-carboxyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t3e | ||||||
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Title | Structure of Thermococcus litoralis Delta(1)-pyrroline-2-carboxylate reductase in complex with NADH and L-proline | ||||||
Components | DELTA1-pyrroline-2-carboxylate reductase | ||||||
Keywords | OXIDOREDUCTASE / Reductase / L-Hydroxyproline metabolism / Delta(1)-pyrroline-2-carboxylate / Thermococcus litoralis | ||||||
Function / homology | Function and homology information ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermococcus litoralis DSM 5473 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ferraris, D.M. / Miggiano, R. / Ferrario, E. / Rizzi, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structure of Thermococcus litoralis Delta1-pyrroline-2-carboxylate reductase in complex with NADH and L-proline. Authors: Ferrario, E. / Miggiano, R. / Rizzi, M. / Ferraris, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t3e.cif.gz | 311 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t3e.ent.gz | 210.9 KB | Display | PDB format |
PDBx/mmJSON format | 6t3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/6t3e ftp://data.pdbj.org/pub/pdb/validation_reports/t3/6t3e | HTTPS FTP |
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-Related structure data
Related structure data | 1omoS 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 domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 38272.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus litoralis DSM 5473 (archaea) Production host: Escherichia coli (E. coli) References: UniProt: H3ZMH3*PLUS, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.32 Å3/Da / Density % sol: 47.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.8 Details: 0.2 M Potassium nitrate pH=6.8, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43.8 Å / Num. all: 93981 / Num. obs: 20334 / % possible obs: 94.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 45.13 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.12 / Net I/σ(I): 11.05 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.64 / Num. unique all: 9154 / Num. unique obs: 2015 / CC1/2: 0.6 / Rpim(I) all: 0.44 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OMO Resolution: 2.6→43.77 Å / SU ML: 0.3294 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1516
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.87 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.733 Å
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Refinement TLS params. | Method: refined / Origin x: 21.9355010513 Å / Origin y: -1.31258423856 Å / Origin z: -2.04954543162 Å
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Refinement TLS group | Selection details: all |