[English] 日本語
Yorodumi- PDB-4njj: Crystal Structure of QueE from Burkholderia multivorans in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4njj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 6-carboxy-5,6,7,8-tetrahydropterin, and Manganese(II) | ||||||
Components | 7-carboxy-7-deazaguanine synthase | ||||||
Keywords | LYASE / AdoMet radical enzyme / modified partial TIM barrel-like structure / radical SAM fold / radical AdoMet fold / synthase | ||||||
Function / homology | Function and homology information 7-carboxy-7-deazaguanine synthase / carbon-nitrogen lyase activity / queuosine biosynthetic process / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Burkholderia multivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Dowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4njj.cif.gz | 102 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4njj.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 4njj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4njj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4njj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4njj_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4njj_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/4njj ftp://data.pdbj.org/pub/pdb/validation_reports/nj/4njj | HTTPS FTP |
-Related structure data
Related structure data | 4njgSC 4njhC 4njiC 4njkC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / 249 / Gene: queE, Bmul_3115, BMULJ_00116 / Production host: Escherichia coli (E. coli) References: UniProt: A9AC61, UniProt: A0A0H3KB22*PLUS, 7-carboxy-7-deazaguanine synthase |
---|
-Non-polymers , 5 types, 79 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.65 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.7399 Å |
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: 1.7399 Å / Relative weight: 1 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|