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Yorodumi- PDB-1c3v: DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3v | ||||||
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Title | DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND PDC | ||||||
Components | DIHYDRODIPICOLINATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / TWO-DOMAIN STRUCTURE / 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 / Resolution: 2.39 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 | 1c3v.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3v.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c3v_validation.pdf.gz | 1017.2 KB | Display | wwPDB validaton report |
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Full document | 1c3v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1c3v_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 1c3v_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3v ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3v | HTTPS FTP |
-Related structure data
-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 dimer constructed from chain A by a non-crystallographic binary 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) / Plasmid: PET23A / Production host: Escherichia coli (E. coli) 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: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: May 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30.4 Å / Num. all: 19713 / Num. obs: 16553 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.29 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.11 |
Reflection shell | Resolution: 2.54→2.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.395 / Num. unique all: 3306 / % possible all: 88.68 |
-Processing
Software |
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Refinement | Resolution: 2.39→30.4 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber Details: Used torsion-angle molecular dynamics slowcool followed by B factor and positional refinements as implemented in X-PLOR.
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Refinement step | Cycle: LAST / Resolution: 2.39→30.4 Å
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Refine LS restraints |
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