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- PDB-1ixe: Crystal structure of citrate synthase from Thermus thermophilus HB8 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ixe | ||||||
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Title | Crystal structure of citrate synthase from Thermus thermophilus HB8 | ||||||
![]() | citrate synthase | ||||||
![]() | LYASE / enzyme-products complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murakami, M. / Kanamori, E. / Kawaguchi, S. / Kuramitsu, S. / Kouyama, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structural comparison between the open and closed forms of citrate synthase from Thermus thermophilus HB8. Authors: Kanamori, E. / Kawaguchi, S. / Kuramitsu, S. / Kouyama, T. / Murakami, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308.2 KB | Display | ![]() |
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PDB format | ![]() | 250.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 66.1 KB | Display | |
Data in CIF | ![]() | 87.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iomSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a homodimer generated from the monomer in the asymmetric unit by the operations: y, x, -z. |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 42362.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9LCX9, UniProt: Q5SIM6*PLUS, EC: 4.1.3.7 |
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-Non-polymers , 5 types, 539 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-COA / #4: Chemical | ChemComp-CIT / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: lithium sulfate, sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 28, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→24.12 Å / Num. all: 73387 / Num. obs: 66309 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8335 / Rsym value: 0.217 / % possible all: 76.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IOM Resolution: 2.3→14.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1489795.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.8 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→14.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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