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- PDB-1h60: Structure of Pentaerythritol Tetranitrate Reductase in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h60 | ||||||
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Title | Structure of Pentaerythritol Tetranitrate Reductase in complex with progesterone | ||||||
![]() | PENTAERYTHRITOL TETRANITRATE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / STEROID BINDING / FLAVOENZYME | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Barna, T.M. / Moody, P.C.E. | ||||||
![]() | ![]() Title: Crystal Structure of Pentaerythritol Tetranitrate Reductase: "Flipped" Binding Geometries for Steroid Substrates in Different Redox States of the Enzyme Authors: Barna, T.M. / Khan, H. / Bruce, N.C. / Barsukov, I. / Scrutton, N.S. / Moody, P.C. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h50C ![]() 1h51C ![]() 1h61C ![]() 1h62C ![]() 1h63C ![]() 1oyaS 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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Unit cell |
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Components
#1: Protein | Mass: 39404.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NON-COVALENTLY BOUND FLAVIN MONONUCLEOTIDE / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-STR / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 22% PEG 2000, 0.1M CACODYLIC ACID, PH 6.0, 0.1M SODIUM CITRATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / pH: 6.2 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 46673 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 8 / % possible all: 94.2 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 595486 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS Rmerge(I) obs: 0.172 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OYA Resolution: 1.6→31 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1370935.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 31 Å / Rfactor obs: 0.198 / Rfactor Rfree: 0.239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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