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- PDB-6y01: The structure of the molybdenum cofactor binding protein from the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y01 | ||||||
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Title | The structure of the molybdenum cofactor binding protein from the phototrophic bacterium Rippkaea orientalis | ||||||
![]() | p450 cytochrome, putative | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | Conserved hypothetical protein CHP00725 / SLOG cluster4 / SLOG cluster4 family / ![]() ![]() | ||||||
Biological species | Rippkaea orientalis | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krausze, J. | ||||||
![]() | ![]() Title: The structure of the Moco carrier protein from Rippkaea orientalis. Authors: Krausze, J. / Hercher, T.W. / Archna, A. / Kruse, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2iz6S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
#1: Protein | Mass: 18893.697 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PCC8801_2644 / Plasmid: pQE80 / Cell line (production host): RK5204 / Production host: ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-CL / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % / Description: rod-like, monoclinic |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 15% (v/v) Pentaerythritol ethoxylate; 0.2 M potassium acetate; 3% (v/v) Jeffamine T-403; 0.1 M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 17, 2015 / Details: TOROIDAL FOCUSING MIRRORS |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.23→64.52 Å / Num. obs: 181674 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 15.66 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05279 / Rpim(I) all: 0.02177 / Rrim(I) all: 0.05719 / Net I/σ(I): 16.35 |
Reflection shell | Resolution: 1.23→1.274 Å / Redundancy: 6.3 % / Rmerge(I) obs: 3.026 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 18104 / CC1/2: 0.193 / CC star: 0.569 / Rpim(I) all: 1.297 / Rrim(I) all: 3.299 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2IZ6 Resolution: 1.23→64.518 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 3.314 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 Details: Hydrogens have been added in their riding positions. Paired refinement was carried out to evaluate the proper high-resolution limit.
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.869 Å2
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Refinement step | Cycle: LAST / Resolution: 1.23→64.518 Å
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Refine LS restraints |
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