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Yorodumi- PDB-7e8n: Crystal structure of Type II citrate synthase (HyCS) from Hymenob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e8n | ||||||
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Title | Crystal structure of Type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554 | ||||||
Components | Citrate synthase | ||||||
Keywords | TRANSFERASE / citrate synthase / Hymenobacter sp. PAMC 26554 / domain movement / RIBOSOMAL PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Hymenobacter sp. PAMC 26554 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Park, S.-H. / Lee, C.W. / Bae, D.-W. / Lee, J.H. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2021 Title: Structural basis of the cooperative activation of type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554. Authors: Park, S.H. / Lee, C.W. / Bae, D.W. / Do, H. / Jeong, C.S. / Hwang, J. / Cha, S.S. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e8n.cif.gz | 264.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e8n.ent.gz | 213.6 KB | Display | PDB format |
PDBx/mmJSON format | 7e8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/7e8n ftp://data.pdbj.org/pub/pdb/validation_reports/e8/7e8n | HTTPS FTP |
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-Related structure data
Related structure data | 4tvmS S: Starting model for refinement |
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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: 48358.984 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hymenobacter sp. PAMC 26554 (bacteria) / Gene: gltA, A0257_01235 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A142HAE2 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.6 Å3/Da / Density % sol: 52.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium cacodylate, HCl (pH 6.5), 1 M sodium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 76885 / % possible obs: 99.8 % / Redundancy: 7.9 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 47.2 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.342 / Num. unique obs: 3807 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TVM Resolution: 2.2→41.58 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.851 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.45 Å2 / Biso mean: 46.798 Å2 / Biso min: 14.78 Å2
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Refinement step | Cycle: final / Resolution: 2.2→41.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.254 Å / Rfactor Rfree error: 0
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