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Yorodumi- PDB-1ixe: Crystal structure of citrate synthase from Thermus thermophilus HB8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ixe | ||||||
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Title | Crystal structure of citrate synthase from Thermus thermophilus HB8 | ||||||
Components | citrate synthase | ||||||
Keywords | LYASE / enzyme-products complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Murakami, M. / Kanamori, E. / Kawaguchi, S. / Kuramitsu, S. / Kouyama, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Biophys Physicobio. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ixe.cif.gz | 308.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ixe.ent.gz | 250.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ixe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/1ixe ftp://data.pdbj.org/pub/pdb/validation_reports/ix/1ixe | HTTPS FTP |
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-Related structure data
Related structure data | 1iomSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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. |
-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.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) References: UniProt: Q9LCX9, UniProt: Q5SIM6*PLUS, EC: 4.1.3.7 |
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-Non-polymers , 5 types, 539 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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