+Open data
-Basic information
Entry | Database: PDB / ID: 4d0r | ||||||
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Title | Mtb InhA complex with Pyradizinone compound 1 | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
Keywords | OXIDOREDUCTASE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Read, J.A. / Gingell, H. / 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 | 4d0r.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d0r.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 4d0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d0r_validation.pdf.gz | 943 KB | Display | wwPDB validaton report |
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Full document | 4d0r_full_validation.pdf.gz | 944.6 KB | Display | |
Data in XML | 4d0r_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4d0r_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d0r ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d0r | HTTPS FTP |
-Related 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: 28555.766 Da / Num. of mol.: 1 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) |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-41I / |
#4: 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: 3.31 Å3/Da / Density % sol: 62.82 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Feb 7, 2013 / Details: MIRRORS |
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: 2.75→84 Å / Num. obs: 10586 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 70.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.75→2.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→84 Å / Cor.coef. Fo:Fc: 0.9258 / Cor.coef. Fo:Fc free: 0.9168 / SU R Cruickshank DPI: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.6 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.291
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Displacement parameters | Biso mean: 54.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→3.07 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 51.6739 Å / Origin y: 47.3038 Å / Origin z: 18.5353 Å
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Refinement TLS group | Selection details: CHAIN A |