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- PDB-6h9f: Structure of glutamate mutase reconstituted with bishomo-coenzyme B12 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h9f | ||||||
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Title | Structure of glutamate mutase reconstituted with bishomo-coenzyme B12 | ||||||
![]() | (Glutamate mutase ...) x 2 | ||||||
![]() | ISOMERASE / COENZYME B12 / CO-C-BOND / RADICAL REACTION / TIM-BARREL / ROSSMAN-FOLD | ||||||
Function / homology | ![]() methylaspartate mutase / anaerobic glutamate catabolic process / methylaspartate mutase activity / glutamate catabolic process via L-citramalate / cobalamin binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gruber, K. / Csitkovits, V. / Kratky, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. Authors: Gruber, K. / Csitkovits, V. / Lyskowski, A. / Kratky, C. / Krautler, 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 | ![]() | 354.5 KB | Display | ![]() |
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PDB format | ![]() | 227.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 59 KB | Display | |
Data in CIF | ![]() | 88.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h9eC ![]() 1ccwS 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
-Glutamate mutase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 14830.991 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: small subunit / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 53614.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: large subunit / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 1360 molecules ![](data/chem/img/B12.gif)
![](data/chem/img/8ZB.gif)
![](data/chem/img/TAR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/8ZB.gif)
![](data/chem/img/TAR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 6% (w/v) PEG-4000, 0.1 M DL-tartrate, pH=4.5, 2 mM CdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35.4 Å / Num. obs: 88205 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.74 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.1228 / Rrim(I) all: 0.241 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6425 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 33437 / CC1/2: 0.679 / Rpim(I) all: 0.3826 / Rrim(I) all: 0.7488 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ccw Resolution: 2.1→35.35 Å / SU ML: 0.2226 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1106
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→35.35 Å
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Refine LS restraints |
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LS refinement shell |
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