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- PDB-1lkm: Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lkm | ||||||
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Title | Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(III) form | ||||||
![]() | Rubrerythrin all-iron(III) form | ||||||
![]() | ELECTRON TRANSPORT / Rubrerythrin / oxidized form / diiron / four-helix bundle / rubredoxin-like | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jin, S. / Kurtz Jr., D.M. / Liu, Z.J. / Rose, J. / Wang, B.C. | ||||||
![]() | ![]() Title: X-ray Crystal Structures of Reduced Rubrerythrin and its Azide Adduct: A Structure-Based Mechanism for a Non-Heme DiIron Peroxidase Authors: Jin, S. / Kurtz Jr., D.M. / Liu, Z.J. / Rose, J. / Wang, B.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.9 KB | Display | ![]() |
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PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1lkoC ![]() 1lkpC ![]() 1rytS 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: 21577.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1450, Tris, Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Details: deMare, F., (1996) Nature Struct. Biol., 3, 539. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2000 / Details: Confocal Maxflux Optics |
Radiation | Monochromator: Confocal Maxflux Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. all: 21378 / Num. obs: 21378 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 44.8 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1564 / % possible all: 70.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 21164 / % possible obs: 93.7 % / Num. measured all: 257523 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS Rmerge(I) obs: 0.209 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1RYT Resolution: 1.69→25.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 557053.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.2517 Å2 / ksol: 0.332825 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.69→25.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.8 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rfree: 0.2102 / Rfactor Rwork: 0.1896 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.309 / Rfactor Rwork: 0.324 |