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Yorodumi- PDB-1zrr: Residual Dipolar Coupling Refinement of Acireductone Dioxygenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zrr | |||||||||
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Title | Residual Dipolar Coupling Refinement of Acireductone Dioxygenase from Klebsiella | |||||||||
Components | E-2/E-2' protein | |||||||||
Keywords | OXIDOREDUCTASE / nickel / cupin / beta helix / methionine salvage | |||||||||
Function / homology | Function and homology information acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / nickel cation binding / iron ion binding Similarity search - Function | |||||||||
Biological species | Klebsiella oxytoca (bacteria) | |||||||||
Method | SOLUTION NMR / combined torsional, cartesian dynamics simulated annealing with residual dipolar couplings, NOE, chemical shift, dihedral restraints | |||||||||
Authors | Pochapsky, T.C. / Pochapsky, S.S. / Ju, T. / Hoefler, C. / Liang, J. | |||||||||
Citation | Journal: J.Biomol.NMR / Year: 2006 Title: A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings Authors: Pochapsky, T.C. / Pochapsky, S.S. / Ju, T. / Hoefler, C. / Liang, J. #1: Journal: Nat.Struct.Biol. / Year: 2002 Title: Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae Authors: Pochapsky, T.C. / Pochapsky, S.S. / Ju, T. / Mo, H. / Al-Mjeni, F. / Maroney, M.J. #2: Journal: Biochemistry / Year: 2001 Title: Mechanistic Studies of two Dioxygenases from the methionine salvage pathway of Klebsiella pneumoniae Authors: Dai, Y. / Pochapsky, T.C. / Abeles, R.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zrr.cif.gz | 921.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zrr.ent.gz | 784.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zrr_validation.pdf.gz | 343.9 KB | Display | wwPDB validaton report |
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Full document | 1zrr_full_validation.pdf.gz | 545.4 KB | Display | |
Data in XML | 1zrr_validation.xml.gz | 84 KB | Display | |
Data in CIF | 1zrr_validation.cif.gz | 110.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/1zrr ftp://data.pdbj.org/pub/pdb/validation_reports/zr/1zrr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20219.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZFE7 |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Details | Contents: 1 mM aRD 15N labeled in 5% orienting medium (either filamentous phage or C12E5 polymer) pH 7.4, 20 mM KPi; 90/10 H2O/D2O Solvent system: 90/10 H2O/D2O |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software | Name: X-PLOR / Version: 2.1 / Classification: refinement |
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Refinement | Method: combined torsional, cartesian dynamics simulated annealing with residual dipolar couplings, NOE, chemical shift, dihedral restraints Software ordinal: 1 Details: Metal binding site modeled from XAFS data, paramagnetically broadened backbone residues modeled from pdb entry 1VR3 (ARD homologue from Mus musculus). |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformers submitted total number: 17 |