+Open data
-Basic information
Entry | Database: PDB / ID: 7xdu | ||||||
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Title | TtherAmDH-NAD+ | ||||||
Components | 4-hydroxy-tetrahydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE / Complex | ||||||
Function / homology | 2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / 4-hydroxy-tetrahydrodipicolinate reductase / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / lysine biosynthetic process via diaminopimelate / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-hydroxy-tetrahydrodipicolinate reductase Function and homology information | ||||||
Biological species | Thermoanaerobacter thermohydrosulfuricus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Chen, C. / Qian, Y.Y. / Pan, J. / Bai, Y.P. / Xu, J.H. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Stereoselective synthesis of chiral lactams via an engineered natural amine dehydrogenase. Authors: Chen, C. / Qian, Y.Y. / Pan, J. / Xu, J.H. / Bai, Y.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xdu.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xdu.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 7xdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/7xdu ftp://data.pdbj.org/pub/pdb/validation_reports/xd/7xdu | HTTPS FTP |
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-Related structure data
Related structure data | 6g1mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38417.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter thermohydrosulfuricus (bacteria) Gene: SAMN04244560_00044, SAMN04324257_01069 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I1Z0X1 #2: Chemical | #3: 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: 3.73 Å3/Da / Density % sol: 67.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: sodium malonate dibasic onohydrate, Bis-Tris propane, PEG 3350 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 35169 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.057 / Rrim(I) all: 0.149 / Χ2: 0.996 / Net I/σ(I): 6.8 / Num. measured all: 241862 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G1M Resolution: 2.6→45.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.05 Å2 / Biso mean: 42.8694 Å2 / Biso min: 15.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→45.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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