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- PDB-4njj: Crystal Structure of QueE from Burkholderia multivorans in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4njj | ||||||
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Title | Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 6-carboxy-5,6,7,8-tetrahydropterin, and Manganese(II) | ||||||
![]() | 7-carboxy-7-deazaguanine synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L. | ||||||
![]() | ![]() Title: Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. Authors: Dowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4njgSC ![]() 4njhC ![]() 4njiC ![]() 4njkC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 25343.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: A9AC61, UniProt: A0A0H3KB22*PLUS, ![]() |
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-Non-polymers , 5 types, 79 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/2K8.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/2K8.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | #5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.65 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: anaerobic, crystals formed in 2.0 M sodium dipotassium phosphate, pH 6.8, 0.1 M sodium acetate, pH 4.5, buffer-exchanged into 0.1 M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, 0.1 M manganese ...Details: anaerobic, crystals formed in 2.0 M sodium dipotassium phosphate, pH 6.8, 0.1 M sodium acetate, pH 4.5, buffer-exchanged into 0.1 M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, 0.1 M manganese sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2012 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→48.2 Å / Num. obs: 21371 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 63.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.551 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4NJG Resolution: 2.7→48.163 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 21.11 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.163 Å
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Refine LS restraints |
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LS refinement shell |
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