+Open data
-Basic information
Entry | Database: PDB / ID: 8i78 | ||||||
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Title | Meso-Diaminopimelate dehydrogenase | ||||||
Components | Meso-diaminopimelate D-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / oxidordeuctase / Meso-Diaminopimelate dehydrogenase / D-Amino acid / Reductive amination | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Wei, S. / Wu, T.F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Analysis of the catalytic mechanism of meso-DAPDH and extension of D-aromatic amino acid substrate scope Authors: wu, T.F. / wei, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i78.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i78.ent.gz | 192.6 KB | Display | PDB format |
PDBx/mmJSON format | 8i78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i78_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 8i78_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 8i78_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 8i78_validation.cif.gz | 65.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/8i78 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/8i78 | HTTPS FTP |
-Related structure data
Related structure data | 8i7hC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 32274.896 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: EKQ45_05540 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A857SCE6 #2: 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: 4.11 Å3/Da / Density % sol: 70.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 2M ammonium sulfate, 0.1M Sodium acetate trihydrate, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jun 25, 2021 / Details: multilayer |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→47.48 Å / Num. obs: 58941 / % possible obs: 99.97 % / Redundancy: 5.13 % / CC1/2: 0.995 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.64→2.71 Å / Num. unique obs: 4572 / CC1/2: 0.689 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→47.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.086 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.23 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.672 Å2
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Refinement step | Cycle: 1 / Resolution: 2.64→47.52 Å
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Refine LS restraints |
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