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Yorodumi- PDB-1yl6: crystal structure of Mycobacterium tuberculosis dihydrodipicolina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yl6 | ||||||
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Title | crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B) | ||||||
Components | Dihydrodipicolinate reductase4-hydroxy-tetrahydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE / lysine biosynthesis / dihydrodipicolinate / reductase / NADH / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
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 / cell wall / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Janowski, R. / Kefala, G. / Weiss, M.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms. Authors: Janowski, R. / Kefala, G. / Weiss, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yl6.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yl6.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/1yl6 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/1yl6 | HTTPS FTP |
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-Related structure data
Related structure data | 1yl5C 1yl7C 1p9lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 40 - 242 / Label seq-ID: 40 - 242
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Details | THE SECOND PART OF THE BIOLOGICAL ASSEMBLY (TETRAMER) IS GENERATED BY THE TWO FOLD AXIS: 1/2, 1/2, Z. |
-Components
#1: Protein | Mass: 25703.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dapB / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP References: UniProt: P72024, UniProt: P9WP23*PLUS, EC: 1.3.1.26 #2: Chemical | #3: 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: 2.9 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris/HCl, 24 % PEG 3350, 140 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 15, 2003 |
Radiation | Monochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→99 Å / Num. all: 13831 / Num. obs: 13831 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 31.1 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.9→2.95 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4 / Num. unique all: 657 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P9L Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 38.566 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.521 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.9→3.055 Å / Total num. of bins used: 10
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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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