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Yorodumi- PDB-1p9l: Structure of M. tuberculosis dihydrodipicolinate reductase in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p9l | ||||||
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Title | Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 PDC | ||||||
Components | dihydrodipicolinate reductase4-hydroxy-tetrahydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE / REDUCTASE / LYSINE BIOSYNTHESIS / NADH BINDING SPECIFICITY / TB Structural Genomics Consortium / TBSGC / Structural Genomics / PSI / Protein Structure Initiative | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity. Authors: Cirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p9l.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p9l.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 1p9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p9l ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p9l | HTTPS FTP |
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-Related structure data
Related structure data | 1c3vC 1arzS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is a tetramer, generated by a crystallographic two-fold axis |
-Components
#1: Protein | Mass: 25793.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dapB / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P72024, UniProt: P9WP23*PLUS, EC: 1.3.1.26 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: 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: 2.66 Å3/Da / Density % sol: 53.78 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium Sulfate, PEG 400, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 12, 1996 |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 24785 / Num. obs: 24502 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.078 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2353 / Rsym value: 0.206 / % possible all: 95.1 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 77959 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 95.1 % / Redundancy: 2.1 % / Num. unique obs: 2353 / Num. measured obs: 4910 / Rmerge(I) obs: 0.206 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ARZ Resolution: 2.3→25 Å / Data cutoff high absF: 0.001 / Data cutoff low absF: 10000000 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.8 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å
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Refinement | *PLUS Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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