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Yorodumi- PDB-7mss: Human E105Qa GTP-specific succinyl-CoA synthetase complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mss | ||||||
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Title | Human E105Qa GTP-specific succinyl-CoA synthetase complexed with succinate, magnesium ion and CoA | ||||||
Components | (Succinate--CoA ligase ...) x 2 | ||||||
Keywords | LIGASE / Complex | ||||||
Function / homology | Function and homology information succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate metabolic process / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / succinyl-CoA catabolic process ...succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate metabolic process / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / succinyl-CoA catabolic process / Citric acid cycle (TCA cycle) / tricarboxylic acid cycle / Mitochondrial protein degradation / GDP binding / mitochondrial matrix / nucleotide binding / protein-containing complex binding / GTP binding / magnesium ion binding / mitochondrion / RNA binding / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Huang, J. / Fraser, M.E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase Authors: Huang, J. / Fraser, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mss.cif.gz | 269.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mss.ent.gz | 216.3 KB | Display | PDB format |
PDBx/mmJSON format | 7mss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mss_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7mss_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7mss_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 7mss_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/7mss ftp://data.pdbj.org/pub/pdb/validation_reports/ms/7mss | HTTPS FTP |
-Related structure data
Related structure data | 7msrC 7mstC 5caeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Succinate--CoA ligase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33526.363 Da / Num. of mol.: 1 / Mutation: E105Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P53597, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming) |
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#2: Protein | Mass: 42627.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q96I99, succinate-CoA ligase (GDP-forming) |
-Non-polymers , 6 types, 281 molecules
#3: Chemical | ChemComp-COA / | ||||||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-SIN / | #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
-Details
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: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 22.5% (w/v) PEG3350, 100 mM Ammonium succinate pH 7.5, 100 mM Tris-HCl 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 28, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.75→56.32 Å / Num. obs: 66677 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.28 Å2 / Rpim(I) all: 0.051 / Rrim(I) all: 0.093 / Net I/σ(I): 12.4 / Num. measured all: 215571 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CAE Resolution: 1.75→53.01 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.84 Å2 / Biso mean: 42.4354 Å2 / Biso min: 18.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→53.01 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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