+Open data
-Basic information
Entry | Database: PDB / ID: 6opl | ||||||
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Title | Human biliverdin IX beta reductase Q14R mutant: NADP complex | ||||||
Components | Flavin reductase (NADPH) | ||||||
Keywords | OXIDOREDUCTASE / Human biliverdin IX beta reductase / short-chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information biliberdin reductase NAD+ activity / biliverdin reductase (NADPH) activity / biliverdin reductase / biliverdin reductase (NAD(P)H) activity / flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / terminal bouton / Cytoprotection by HMOX1 ...biliberdin reductase NAD+ activity / biliverdin reductase (NADPH) activity / biliverdin reductase / biliverdin reductase (NAD(P)H) activity / flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / terminal bouton / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Paukovich, N.A. / Eisenmesser, E.Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Controlling biliverdin reductase B coenzyme binding through evolution Authors: Paukovich, N.A. / Eisenmesser, E.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6opl.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6opl.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 6opl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/6opl ftp://data.pdbj.org/pub/pdb/validation_reports/op/6opl | HTTPS FTP |
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-Related structure data
Related structure data | 1hdoS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22049.283 Da / Num. of mol.: 1 / Mutation: Q14R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR / Production host: Escherichia coli (E. coli) References: UniProt: P30043, flavin reductase (NADPH), biliverdin reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: mother liquor: 0.1 M MES monohydrate, 12% w/v PEG20000, 1 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 24, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→39.98 Å / Num. obs: 55280 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Χ2: 0.97 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 4 % / Rmerge(I) obs: 2.133 / Num. unique obs: 2685 / CC1/2: 0.317 / Χ2: 0.73 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HDO Resolution: 1.37→38.697 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→38.697 Å
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Refine LS restraints |
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LS refinement shell |
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