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Yorodumi- PDB-1hdr: THE CRYSTALLOGRAPHIC STRUCTURE OF A HUMAN DIHYDROPTERIDINE REDUCT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hdr | ||||||
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Title | THE CRYSTALLOGRAPHIC STRUCTURE OF A HUMAN DIHYDROPTERIDINE REDUCTASE NADH BINARY COMPLEX EXPRESSED IN ESCHERICHIA COLI BY A CDNA CONSTRUCTED FROM ITS RAT HOMOLOGUE | ||||||
Components | DIHYDROPTERIDINE REDUCTASE6,7-dihydropteridine reductase | ||||||
Keywords | OXIDOREDUCTASE(ACTING ON NADH) | ||||||
Function / homology | Function and homology information dihydrobiopterin metabolic process / 6,7-dihydropteridine reductase / cellular response to xenobiotic stimulus => GO:0071466 / 6,7-dihydropteridine reductase activity / Phenylalanine metabolism / NADH binding / response to aluminum ion / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / response to glucagon ...dihydrobiopterin metabolic process / 6,7-dihydropteridine reductase / cellular response to xenobiotic stimulus => GO:0071466 / 6,7-dihydropteridine reductase activity / Phenylalanine metabolism / NADH binding / response to aluminum ion / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / response to glucagon / amino acid metabolic process / NADPH binding / liver development / response to lead ion / electron transfer activity / neuron projection / extracellular exosome / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Varughese, K.I. / Su, Y. / Xuong, N.H. / Whiteley, J.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: The crystallographic structure of a human dihydropteridine reductase NADH binary complex expressed in Escherichia coli by a cDNA constructed from its rat homologue. Authors: Su, Y. / Varughese, K.I. / Xuong, N.H. / Bray, T.L. / Roche, D.J. / Whiteley, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hdr.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hdr.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hdr ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hdr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25816.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / References: UniProt: P09417, 1.6.99.7 |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.34 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 7999 / % possible obs: 97 % / Redundancy: 4.8 % / Num. measured all: 38602 / Rmerge(I) obs: 0.0736 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.69 Å / Num. unique obs: 1451 / Num. measured obs: 3355 / Rmerge(I) obs: 0.1802 |
-Processing
Software |
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Refinement | Resolution: 2.5→8 Å / Rfactor Rwork: 0.169 / Rfactor obs: 0.169 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.2 |