+Open data
-Basic information
Entry | Database: PDB / ID: 8g8k | ||||||
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Title | Crystal structure of Rv1916 (residues 233-398) | ||||||
Components | Putative isocitrate lyase subunit B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Isocitrate lyase / tuberculosis | ||||||
Function / homology | isocitrate lyase / isocitrate lyase activity / Isocitrate lyase / Isocitrate lyase family / carboxylic acid metabolic process / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / DI(HYDROXYETHYL)ETHER / Putative isocitrate lyase subunit B Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Kwai, B.X.C. / Bashiri, G. / Leung, I.K.H. | ||||||
Funding support | 1items
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Citation | Journal: Chembiochem / Year: 2023 Title: Mycobacterium tuberculosis Rv1916 is an Acetyl-CoA-Binding Protein. Authors: Huang, E.Y. / Kwai, B.X.C. / Bhusal, R.P. / Bashiri, G. / Leung, I.K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g8k.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g8k.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 8g8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g8k_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8g8k_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8g8k_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 8g8k_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/8g8k ftp://data.pdbj.org/pub/pdb/validation_reports/g8/8g8k | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18850.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: aceAb, Rv1916, RVBD_1916, LH57_10435, P425_01981 / Production host: Escherichia coli (E. coli) / References: UniProt: O07717, isocitrate lyase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG3350, 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane pH 7.5 |
-Data collection
Diffraction | Mean temperature: 85 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953724 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→46.89 Å / Num. obs: 41501 / % possible obs: 100 % / Redundancy: 26.6 % / CC1/2: 0.999 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.54→1.57 Å / Num. unique obs: 2033 / CC1/2: 0.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→46.89 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.193 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.503 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→46.89 Å
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Refine LS restraints |
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LS refinement shell |
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