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- PDB-7kc7: Biotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kc7 | ||||||
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Title | Biotin Carboxylase domain of Thermophilic 2-Oxoglutarate Carboxylase bound to ADP without Magnesium with disordered phosphate tail | ||||||
![]() | 2-oxoglutarate carboxylase small subunit | ||||||
![]() | LIGASE / biotin carboxylase / biotin-dependent carboxylase / pyruvate carboxylase / ATP-grasp / Aquificales / rTCA / dimer interface / bicarbonate / Sequence Determining Positions / structural waters / thermophile / carbon fixation / thermophilic protein / dimer / wet interface | ||||||
Function / homology | ![]() 2-oxoglutarate carboxylase / 2-oxoglutarate carboxylase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Nucleotide free dimer with Open Lid domain | ||||||
![]() | Buhrman, G.K. / Rose, R.B. / Enriquez, P. / Truong, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer from Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase. Authors: Buhrman, G. / Enriquez, P. / Dillard, L. / Baer, H. / Truong, V. / Grunden, A.M. / Rose, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 335.6 KB | Display | ![]() |
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PDB format | ![]() | 272.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 701.2 KB | Display | ![]() |
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Full document | ![]() | 708.4 KB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kblC ![]() 7kctC ![]() 1ulzS 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: 55014.836 Da / Num. of mol.: 2 / Fragment: Biotin Carboxylase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cfiB, HTH_1393, Hydth_1383 / Plasmid: pET24b / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, 0.02M Citric Acid, 0.08M Bis-Tris-Propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 50075 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.77 Å2 / Rsym value: 0.112 / Net I/σ(I): 26.54 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 5.9 % / Num. unique obs: 2489 / Rsym value: 1.29 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 1ULZ Resolution: 2.2→44.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.35 / 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: 206.59 Å2 / Biso mean: 52.3385 Å2 / Biso min: 24.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→44.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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