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Yorodumi- PDB-5tjz: Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tjz | ||||||
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Title | Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid | ||||||
Components | 4-hydroxy-tetrahydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE / Lysine Biosynthesis | ||||||
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 / NADH binding / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / NAD binding / NADP binding ...4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / NADH binding / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / NAD binding / NADP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mank, N.J. / Arnette, A.K. / Klapper, V. / Chruszcz, M. | ||||||
Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2021 Title: Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus. Authors: Pote, S. / Kachhap, S. / Mank, N.J. / Daneshian, L. / Klapper, V. / Pye, S. / Arnette, A.K. / Shimizu, L.S. / Borowski, T. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tjz.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tjz.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tjz_validation.pdf.gz | 810.6 KB | Display | wwPDB validaton report |
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Full document | 5tjz_full_validation.pdf.gz | 812.5 KB | Display | |
Data in XML | 5tjz_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5tjz_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tjz ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tjz | HTTPS FTP |
-Related structure data
Related structure data | 5tejC 5tekC 5temC 5tenC 5tjyC 5ugvC 5us6C 1c3vS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25682.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria) Strain: ATCC 25177 / H37Ra / Gene: dapB, MRA_2798 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5U6C6, UniProt: P9WP23*PLUS, 4-hydroxy-tetrahydrodipicolinate reductase |
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-Non-polymers , 9 types, 332 molecules
#2: Chemical | ChemComp-PDC / | ||||||
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#3: Chemical | ChemComp-BEZ / | ||||||
#4: Chemical | ChemComp-IMD / | ||||||
#5: Chemical | ChemComp-NAP / | ||||||
#6: Chemical | ChemComp-AE3 / | ||||||
#7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-SO4 / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Chloride, 0.1 M Bis-Tris pH 6.5, 1.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→30 Å / Num. obs: 52243 / % possible obs: 95.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.054 / Net I/av σ(I): 42.436 / Net I/σ(I): 11.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C3V Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.744 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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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 max: 92.19 Å2 / Biso mean: 29.958 Å2 / Biso min: 17.13 Å2
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Refinement step | Cycle: final / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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