+Open data
-Basic information
Entry | Database: PDB / ID: 4d0s | ||||||
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Title | Mtb InhA complex with Pyradizinone compound 14 | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
Keywords | OXIDOREDUCTASE / INHA / ACP ENOYL REDUCTASE / METHYL-THIAZOLE | ||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Read, J.A. / Breed, J. / Madhavapeddi, P. / Lange, S. | ||||||
Citation | Journal: To be Published Title: Pyridazinones: A Novel Scaffold with Excellent Physicochemical Properties and Safety Profile for a Clinically Validated Target of Mycobacterium Tuberculosis Authors: Lange, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d0s.cif.gz | 397.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d0s.ent.gz | 324 KB | Display | PDB format |
PDBx/mmJSON format | 4d0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d0s_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4d0s_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 4d0s_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 4d0s_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d0s ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d0s | HTTPS FTP |
-Related structure data
Related structure data | 4d0rC 2b35S 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
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR References: UniProt: P9WGR0, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-9G4 / #4: Chemical | #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: 2.12 Å3/Da / Density % sol: 41.96 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.8976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8976 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→55.7 Å / Num. obs: 362563 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 21.23 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.64→1.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.2 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B35 Resolution: 1.64→55.71 Å / Cor.coef. Fo:Fc: 0.9606 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.089
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Displacement parameters | Biso mean: 23.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.202 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→55.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.68 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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