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- PDB-6iva: Crystal structure of the S. typhimurium oxaloacetate decarboxylas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iva | ||||||
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Title | Crystal structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex | ||||||
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![]() | MEMBRANE PROTEIN / decarboxylase sodium pump / biotin-dependent decarboxylase | ||||||
Function / homology | ![]() oxaloacetate decarboxylase (Na+ extruding) / decarboxylation-driven active transmembrane transporter activity / sodium ion transmembrane transporter activity / oxaloacetate decarboxylase activity / sodium ion export across plasma membrane / sodium ion transport / lyase activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, X. / Xiang, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump. Authors: Xin Xu / Huigang Shi / Xiaowen Gong / Pu Chen / Ying Gao / Xinzheng Zhang / Song Xiang / ![]() Abstract: The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell ...The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell membrane. It is composed of 3 subunits: the α subunit catalyzes carboxyl-transfer from oxaloacetate to biotin, the membrane integrated β subunit catalyzes the subsequent carboxyl-biotin decarboxylation and the coupled sodium transport, the γ subunit interacts with the α and β subunits and stabilizes the OAD complex. We present here structure of the OAD βγ sub-complex. The structure revealed that the β and γ subunits form a βγ hetero-hexamer with extensive interactions between the subunits and shed light on the OAD holo-enzyme assembly. Structure-guided functional studies provided insights into the sodium binding sites in the β subunit and the coupling between carboxyl-biotin decarboxylation and sodium transport by the OAD β subunit. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 525.5 KB | Display | ![]() |
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PDB format | ![]() | 443.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 481.1 KB | Display | ![]() |
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Full document | ![]() | 498.3 KB | Display | |
Data in XML | ![]() | 47.5 KB | Display | |
Data in CIF | ![]() | 64.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9743C ![]() 6iwwSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44928.801 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0F7JAV8, UniProt: Q8ZRY4*PLUS, oxaloacetate decarboxylase (Na+ extruding) #2: Protein | Mass: 11137.029 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0F7JC72, UniProt: Q03032*PLUS, oxaloacetate decarboxylase (Na+ extruding) Sequence details | Authors state that this confluence may be a natural occurring mutation that happen to exist in the ...Authors state that this confluence may be a natural occurring mutation that happen to exist in the genomic DNA they used. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium chloride, 0.1 M lithium sulfate, 0.1 M sodium citrate pH 5.5, 25% PEG1000 and 0.125% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 4.4→50 Å / Num. obs: 16715 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Net I/σ(I): 14.99 |
Reflection shell | Resolution: 4.4→4.48 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 834 / CC1/2: 0.549 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IWW Resolution: 4.403→42.191 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.403→42.191 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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