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Yorodumi- PDB-1zx1: Human quinone oxidoreductase 2 (NQO2) in complex with the cytosta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zx1 | ||||||
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Title | Human quinone oxidoreductase 2 (NQO2) in complex with the cytostatic prodrug CB1954 | ||||||
Components | NRH dehydrogenase [quinone] 2 | ||||||
Keywords | OXIDOREDUCTASE / Quinone oxidoreductase 2 / reductions of quinones / dihydronicotinamide ribose / electrondonor / 5-(aziridin-1-yl)-2 / 4-dinitrobenamide (CB1954) / flavin-containing / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / oxidoreductase activity / electron transfer activity / protein homodimerization activity / zinc ion binding / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Jansson, A. / Wu, X. / Kavanagh, K. / Kerr, D. / Knox, R. / Walton, R. / Gunther, U. / Ludwig, C. / Edwards, A. / Arrowsmith, C. ...Jansson, A. / Wu, X. / Kavanagh, K. / Kerr, D. / Knox, R. / Walton, R. / Gunther, U. / Ludwig, C. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Human quinone oxidoreductase 2 (NQO2) in complex with the cytostatic prodrug CB1954 Authors: Jansson, A. / Wu, X. / Kavanagh, K. / Kerr, D. / Knox, R. / Walton, R. / Gunther, U. / Ludwig, C. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zx1.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zx1.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zx1_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1zx1_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1zx1_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1zx1_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/1zx1 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zx1 | HTTPS FTP |
-Related structure data
Related structure data | 1qr2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 25980.533 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: NQO2A-c001 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: P16083, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Hepes, ammonium sulphate, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9001 Å |
Detector | Detector: CCD / Date: Feb 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9001 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 29187 / Num. obs: 29187 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.128 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.411 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QR2 Resolution: 2.16→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.671 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: Individual isotropic B-factor refinement for each atom Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: There is some unidentified density at the N-terminal that was not modeled. Some aminoacids have been truncated due to lack of density. Gly130 is cut out due to disordered density. HYDROGENS ...Details: There is some unidentified density at the N-terminal that was not modeled. Some aminoacids have been truncated due to lack of density. Gly130 is cut out due to disordered density. 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.515 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.16→2.216 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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