+Open data
-Basic information
Entry | Database: PDB / ID: 5ugj | ||||||
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Title | Crystal structure of HTPA Reductase from neisseria meningitidis | ||||||
Components | 4-hydroxy-tetrahydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE / HTPA Reductase Lysine biosynthesis DHDPR | ||||||
Function / homology | Function and homology information 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 / cytosol Similarity search - Function | ||||||
Biological species | Neisseria meningitidis serogroup B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Keown, J.K. / Richards, E.W. / Pearce, F.G. / Goldstone, D.C. | ||||||
Citation | Journal: Biochem. J. / Year: 2018 Title: Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly. Authors: Watkin, S.A.J. / Keown, J.R. / Richards, E. / Goldstone, D.C. / Devenish, S.R.A. / Grant Pearce, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ugj.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ugj.ent.gz | 162.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ugj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ugj_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
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Full document | 5ugj_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 5ugj_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 5ugj_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/5ugj ftp://data.pdbj.org/pub/pdb/validation_reports/ug/5ugj | HTTPS FTP |
-Related structure data
Related structure data | 5u5iC 5u5nC 5ua0C 1arzS S: Starting model for refinement C: citing same article (ref.) |
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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: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 32138.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria) Strain: MC58 / Gene: dapB, NMB0203 / Production host: Escherichia coli (E. coli) References: UniProt: Q9K1F1, 4-hydroxy-tetrahydrodipicolinate reductase #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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.03 mM CaCl2, 0.03 mM MgCl2, 20% v/v PEG 500 MME, 10% w/v PEG 20000, and 0.1 M Trizma/BICINE pH 8.5 |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 16, 2013 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.7→47.44 Å / Num. obs: 30159 / % possible obs: 92 % / Redundancy: 2.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.3 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ARZ Resolution: 2.7→47.44 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 15.881 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 237.57 Å2 / Biso mean: 62.326 Å2 / Biso min: 15.42 Å2
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Refinement step | Cycle: final / Resolution: 2.7→47.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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