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- PDB-5b3u: Crystal structure of biliverdin reductase in complex with NADP+ f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b3u | ||||||
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Title | Crystal structure of biliverdin reductase in complex with NADP+ from Synechocystis sp. PCC 6803 | ||||||
![]() | Biliverdin reductase | ||||||
![]() | TRANSFERASE / biliverdin reductase / heme degrading pathway / NADPH complex / NAD(P)H-dependent enzyme / tetrapyrrole / Rossmann fold | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takao, H. / Wada, K. | ||||||
![]() | ![]() Title: A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity Authors: Takao, H. / Hirabayashi, K. / Nishigaya, Y. / Kouriki, H. / Nakaniwa, T. / Hagiwara, Y. / Harada, J. / Sato, H. / Yamazaki, T. / Sakakibara, Y. / Suiko, M. / Asada, Y. / Takahashi, Y. / ...Authors: Takao, H. / Hirabayashi, K. / Nishigaya, Y. / Kouriki, H. / Nakaniwa, T. / Hagiwara, Y. / Harada, J. / Sato, H. / Yamazaki, T. / Sakakibara, Y. / Suiko, M. / Asada, Y. / Takahashi, Y. / Yamamoto, K. / Fukuyama, K. / Sugishima, M. / Wada, K. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2011 Title: Expression, purification and preliminary X-ray crystallographic analysis of cyanobacterial biliverdin reductase. Authors: Watanabe, A. / Hirata, K. / Hagiwara, Y. / Yutani, Y. / Sugishima, M. / Yamamoto, M. / Fukuyama, K. / Wada, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.7 KB | Display | ![]() |
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PDB format | ![]() | 106.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5b3tSC ![]() 5b3vC C: citing same article ( 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36963.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NAP / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG4000, Tris-HCl (pH7.25), Sodium acetate, Cymal-2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.698→50 Å / Num. obs: 19500 / % possible obs: 99.8 % / Redundancy: 10 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.7→2.86 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 3.47 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B3T Resolution: 2.698→48.622 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.698→48.622 Å
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Refine LS restraints |
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LS refinement shell |
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