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Open data
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Basic information
Entry | Database: PDB / ID: 6n01 | ||||||
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Title | Structure of apo AztD from Citrobacter koseri | ||||||
![]() | AztD Protein | ||||||
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Function / homology | Nitrous oxide reductase, N-terminal / WD40/YVTN repeat-like-containing domain superfamily / ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yukl, E.T. / Neupane, D.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins. Authors: Neupane, D.P. / Fullam, S.H. / Chacon, K.N. / Yukl, E.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 | ![]() | 523.4 KB | Display | ![]() |
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PDB format | ![]() | 433.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ck1C ![]() 6cmkSC S: Starting model for refinement C: citing same article ( |
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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: 45467.371 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_00948 / Production host: ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-MES / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow![]() | Temperature: 292 K / Method: batch mode / pH: 6 Details: 10 mg/mL protein was combined in a 1:1 ratio with 24% PEG 4000, 0.1 M sodium nitrate, 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 PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2018 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.98→48.43 Å / Num. obs: 110365 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Χ2: 0.9 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16782 / CC1/2: 0.758 / Rpim(I) all: 0.326 / Rrim(I) all: 0.621 / Χ2: 0.69 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6cmk Resolution: 1.98→48.431 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.85 / 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: 1.98→48.431 Å
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Refine LS restraints |
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LS refinement shell |
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