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Yorodumi- PDB-1rqd: deoxyhypusine synthase holoenzyme in its low ionic strength, high... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqd | ||||||
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Title | deoxyhypusine synthase holoenzyme in its low ionic strength, high pH crystal form with the inhibitor GC7 bound in the active site | ||||||
Components | Deoxyhypusine synthase | ||||||
Keywords | TRANSFERASE / Rossmann Fold / NAD cofactor / deoxyhypusine / hypusine / spermidine / GC7 | ||||||
Function / homology | Function and homology information deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||
Authors | Umland, T.C. / Wolff, E.C. / Park, M.-H. / Davies, D.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: A New Crystal Structure of Deoxyhypusine Synthase Reveals the Configuration of the Active Enzyme and of an Enzyme-NAD-Inhibitor Ternary Complex Authors: Umland, T.C. / Wolff, E.C. / Park, M.-H. / Davies, D.R. #1: Journal: Structure / Year: 1998 Title: Crystal structure of the NAD complex of human deoxyhypusine synthase: an enzyme with a ball-and-chain mechanism for blocking the active site Authors: Liao, D.I. / Wolff, E. / Park, M.-H. / Davies, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rqd.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqd.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rqd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1rqd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1rqd_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 1rqd_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqd ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqd | HTTPS FTP |
-Related structure data
Related structure data | 1rlzC 1rozSC C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The biological assembly is a tetramer, and may be generated from the dimer contained within the asymmetric unit by the crystallographic two fold axis: x-y, -y, -z+1/3 |
-Components
#1: Protein | Mass: 41012.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49366, deoxyhypusine synthase #2: Chemical | #3: Chemical | |
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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: 3.08 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl, KCl, NAD, 2-methyl-2,4-pentanediol,1-guanidinium-7-aminoheptane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 1999 / Details: monochromator |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 20171 / Num. obs: 20171 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.099 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.8 % / Num. unique all: 1913 / Rsym value: 0.254 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1ROZ Resolution: 3→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.6 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→35 Å
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Refine LS restraints |
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