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Yorodumi- PDB-4quq: Crystal structure of stachydrine demethylase in complex with azide -
+Open data
-Basic information
Entry | Database: PDB / ID: 4quq | ||||||
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Title | Crystal structure of stachydrine demethylase in complex with azide | ||||||
Components | Monoxygenase; demethylaseOxygenase | ||||||
Keywords | OXIDOREDUCTASE / composite datasets / photoelectron / enzyme-catalyzed reactions / azide / synchrotron / Rieske type monoxygenase | ||||||
Function / homology | Function and homology information dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti 1021 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.266 Å | ||||||
Authors | Agarwal, R. / Andi, B. / Gizzi, A. / Bonanno, J.B. / Almo, S.C. / Orville, A.M. | ||||||
Citation | Journal: To be Published Title: Tracking photoelectron induced in-crystallo enzyme catalysis Authors: Agarwal, R. / Andi, B. / Gizzi, A. / Bonanno, J.B. / Almo, S.C. / Orville, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4quq.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4quq.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 4quq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/4quq ftp://data.pdbj.org/pub/pdb/validation_reports/qu/4quq | HTTPS FTP |
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-Related structure data
Related structure data | 4qupC 4qurC 3vcaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49115.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Gene: SMa0751 / Plasmid: pSGC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92ZP9, Oxidoreductases |
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-Non-polymers , 6 types, 160 molecules
#2: Chemical | ChemComp-FES / |
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#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-NCO / |
#6: Chemical | ChemComp-AZI / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5% PEG3350, 10% glycerol, 100 mM HEPES, 25 mM hexamminecobalt chloride, 100 mM sodium azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2013 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 23363 / Num. obs: 23363 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 36.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 35.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5 / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VCA Resolution: 2.266→33.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.036 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.518 Å2
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Refinement step | Cycle: LAST / Resolution: 2.266→33.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.266→2.325 Å / Total num. of bins used: 20
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