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Yorodumi- PDB-2yv1: Crystal Structure of Succinyl-CoA Synthetase Alpha Chain from Met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yv1 | ||||||
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Title | Crystal Structure of Succinyl-CoA Synthetase Alpha Chain from Methanocaldococcus jannaschii DSM 2661 | ||||||
Components | Succinyl-CoA ligase [ADP-forming] subunit alpha | ||||||
Keywords | LIGASE / CoA-binding domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Niwa, H. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Succinyl-CoA Synthetase Alpha Chain from Methanocaldococcus jannaschii DSM 2661 Authors: Niwa, H. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yv1.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yv1.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yv1 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yv1 | HTTPS FTP |
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-Related structure data
Related structure data | 1oi7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30962.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: sucD / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) References: UniProt: Q58643, succinate-CoA ligase (ADP-forming) |
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#2: 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: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M Sodium Acetate, 20% PEG 3350, 0.2M Lithium Sulfate, pH5.6, 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: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 19, 2006 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 31324 / Num. obs: 31324 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 44.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 5.6 / Num. unique all: 3105 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OI7 Resolution: 1.7→29.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1285654.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0151 Å2 / ksol: 0.328966 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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