+Open data
-Basic information
Entry | Database: PDB / ID: 1bi9 | |||||||||
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Title | RETINAL DEHYDROGENASE TYPE TWO WITH NAD BOUND | |||||||||
Components | RETINAL DEHYDROGENASE TYPE II | |||||||||
Keywords | ALDEHYDE DEHYDROGENASE / RETINOID | |||||||||
Function / homology | Function and homology information RA biosynthesis pathway / determination of bilateral symmetry / retinoic acid receptor signaling pathway involved in somitogenesis / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / regulation of endothelial cell proliferation / retinoic acid biosynthetic process / retinal dehydrogenase / embryonic camera-type eye development / ureter maturation ...RA biosynthesis pathway / determination of bilateral symmetry / retinoic acid receptor signaling pathway involved in somitogenesis / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / regulation of endothelial cell proliferation / retinoic acid biosynthetic process / retinal dehydrogenase / embryonic camera-type eye development / ureter maturation / morphogenesis of embryonic epithelium / pituitary gland development / proximal/distal pattern formation / retinal metabolic process / neural crest cell development / hindbrain development / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / cardiac muscle tissue development / camera-type eye development / retinal binding / response to vitamin A / pancreas development / embryonic forelimb morphogenesis / embryonic limb morphogenesis / retinal dehydrogenase activity / neural tube development / retinoic acid metabolic process / retinol metabolic process / anterior/posterior pattern specification / midgut development / blood vessel development / face development / retinoic acid receptor signaling pathway / heart morphogenesis / forebrain development / cellular response to retinoic acid / kidney development / response to cytokine / liver 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Newcomer, M.E. / Lamb, A.L. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 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: Journal: Acta Crystallogr.,Sect.D / Year: 1998 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: Journal: Mech.Dev. / Year: 1997 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: Journal: J.Biol.Chem. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bi9.cif.gz | 337 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bi9.ent.gz | 284.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bi9 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bi9 | HTTPS FTP |
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-Related structure data
Related structure data | 1a4zS 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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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.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Organ: TESTISTesticle / Cell line (production host): BL21 (DE3) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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