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Yorodumi- PDB-5yum: Crystallographic structures of IlvN.Val/Ile complexes:Conformatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yum | ||||||
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Title | Crystallographic structures of IlvN.Val/Ile complexes:Conformational selectivity for feedback inhibition of AHASs | ||||||
Components | Acetolactate synthase isozyme 1 small subunit | ||||||
Keywords | TRANSFERASE / Transferase subunit / Regulatory subunit / ACT protein / amino acid binding | ||||||
Function / homology | Function and homology information acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase complex / branched-chain amino acid biosynthetic process / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.432 Å | ||||||
Authors | Sarma, S.P. / Bansal, A. / Schindelin, H. / Demeler, B. | ||||||
Funding support | India, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases. Authors: Bansal, A. / Karanth, N.M. / Demeler, B. / Schindelin, H. / Sarma, S.P. #1: Journal: Biochemistry / Year: 2013 Title: The coil-to-helix transition in IlvN regulates the allosteric control of Escherichia coli acetohydroxyacid synthase I. Authors: Karanth, N.M. / Sarma, S.P. #2: Journal: Biochemistry / Year: 2008 Title: Escherichia coli ilvN interacts with the FAD binding domain of ilvB and activates the AHAS I enzyme. Authors: Mitra, A. / Sarma, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yum.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yum.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yum ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yum | HTTPS FTP |
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-Related structure data
Related structure data | 5yppC 5ypwC 5ypyC 2lvwS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11262.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ilvN, b3670, JW3645 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADF8, acetolactate synthase |
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#2: Chemical | ChemComp-ILE / |
#3: Chemical | ChemComp-CO / |
#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: 2.98 Å3/Da / Density % sol: 58.73 % |
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Crystal grow | Temperature: 288 K / Method: microbatch / pH: 6.5 Details: 0.01M cobalt(II) chloride hexahydrate, 0.1M MES monohydrate pH 6.5, 1.8M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→57.88 Å / Num. obs: 5202 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.43→2.52 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 534 / CC1/2: 0.949 / Rpim(I) all: 0.195 / Rrim(I) all: 0.037 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LVW Resolution: 2.432→57.878 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.432→57.878 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -3.862 Å / Origin y: 22.5038 Å / Origin z: 1.109 Å
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Refinement TLS group | Selection details: all |