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Open data
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Basic information
Entry | Database: PDB / ID: 1bi9 | |||||||||
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Title | RETINAL DEHYDROGENASE TYPE TWO WITH NAD BOUND | |||||||||
![]() | RETINAL DEHYDROGENASE TYPE II | |||||||||
![]() | ALDEHYDE DEHYDROGENASE / RETINOID | |||||||||
Function / homology | ![]() RA biosynthesis pathway / determination of bilateral symmetry / : / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / regulation of endothelial cell proliferation / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development ...RA biosynthesis pathway / determination of bilateral symmetry / : / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / regulation of endothelial cell proliferation / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / morphogenesis of embryonic epithelium / pituitary gland development / proximal/distal pattern formation / neural crest cell development / retinal metabolic process / hindbrain development / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / camera-type eye development / retinal binding / response to vitamin A / cardiac muscle tissue development / embryonic forelimb morphogenesis / pancreas development / retinal dehydrogenase activity / embryonic limb morphogenesis / neural tube development / retinol metabolic process / retinoic acid metabolic process / anterior/posterior pattern specification / midgut development / blood vessel development / face development / retinoic acid receptor signaling pathway / heart morphogenesis / cellular response to retinoic acid / forebrain development / liver development / response to cytokine / kidney development / lung development / neuron differentiation / response to estradiol / protein homotetramerization / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Newcomer, M.E. / Lamb, A.L. | |||||||||
![]() | ![]() Title: The structure of retinal dehydrogenase type II at 2.7 A resolution: implications for retinal specificity. Authors: Lamb, A.L. / Newcomer, M.E. #1: ![]() Title: Purification, Crystallization and Preliminary X-Ray Diffraction Studies of Retinal Dehydrogenase Type II Authors: Lamb, A.L. / Wang, X. / Napoli, J.L. / Newcomer, M.E. #2: ![]() Title: Restricted Expression and Retinoic Acid-Induced Downregulation of the Retinaldehyde Dehydrogenase Type 2 (Raldh-2) Gene During Mouse Development Authors: Niederreither, K. / Mccaffery, P. / Drager, U.C. / Chambon, P. / Dolle, P. #3: ![]() Title: Cloning of a Cdna Encoding an Aldehyde Dehydrogenase and its Expression in Escherichia Coli. Recognition of Retinal as Substrate Authors: Wang, X. / Penzes, P. / Napoli, J.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337 KB | Display | ![]() |
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PDB format | ![]() | 284.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 622.9 KB | Display | ![]() |
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Full document | ![]() | 703.3 KB | Display | |
Data in XML | ![]() | 48.7 KB | Display | |
Data in CIF | ![]() | 70.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a4zS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 54796.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q63639, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-NAD / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.1 / Details: pH 7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 75572 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 864923 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 3.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A4Z Resolution: 2.7→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 283265.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.49 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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