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- PDB-6bdx: 4-hydroxy tetrahydrodipicolinate reductase from Neisseria gonorrhoeae -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bdx | ||||||
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Title | 4-hydroxy tetrahydrodipicolinate reductase from Neisseria gonorrhoeae | ||||||
![]() | 4-hydroxy-tetrahydrodipicolinate reductase | ||||||
![]() | OXIDOREDUCTASE / Lysine biosynthesis / 4-hydroxy tetrahydrodipicolinate reductase / Neisseria gonorrhoeae | ||||||
Function / homology | ![]() 4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pote, S.S. / Pye, S.E. / Sheahan, T.E. / Chruszcz, M. | ||||||
![]() | ![]() Title: 4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae - structure and interactions with coenzymes and substrate analog. Authors: Pote, S. / Pye, S.E. / Sheahan, T.E. / Gawlicka-Chruszcz, A. / Majorek, K.A. / Chruszcz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.5 KB | Display | ![]() |
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PDB format | ![]() | 85.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1arzS S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 28362.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dapB, WHOK_00270, WHOK_02229C, WHOM_00688, WHOM_02238C, WHOP_00630, WHOP_02238C, WHOU_00751, WHOU_02311C, WHOV_01184, WHOV_02299C, WHOW_00218, WHOW_02292C, WHOX_00871, WHOX_02228C, WHOY_00570, ...Gene: dapB, WHOK_00270, WHOK_02229C, WHOM_00688, WHOM_02238C, WHOP_00630, WHOP_02238C, WHOU_00751, WHOU_02311C, WHOV_01184, WHOV_02299C, WHOW_00218, WHOW_02292C, WHOX_00871, WHOX_02228C, WHOY_00570, WHOY_02311C, WHOZ_01787, WHOZ_02300C Production host: ![]() ![]() References: UniProt: A0A1D3EVW8, UniProt: Q5F5Y7*PLUS, 4-hydroxy-tetrahydrodipicolinate reductase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 25492 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.024 / Rrim(I) all: 0.067 / Rsym value: 0.061 / Net I/σ(I): 48.2 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 3.38 / Num. unique obs: 1251 / Rpim(I) all: 0.27 / Rrim(I) all: 0.757 / Rsym value: 0.784 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ARZ Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.117 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.09 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→40 Å
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Refine LS restraints |
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