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Open data
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Basic information
Entry | Database: PDB / ID: 1m1y | ||||||
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Title | Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein | ||||||
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![]() | OXIDOREDUCTASE / nitrogenase / nitrogen fixation / chemical crosslink / protein interaction | ||||||
Function / homology | ![]() molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmid, B. / Einsle, O. / Chiu, H.J. / Willing, A. / Yoshida, M. / Howard, J.B. / Rees, D.C. | ||||||
![]() | ![]() Title: Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the ADP-AlF4- Stabilized Structure Authors: Schmid, B. / Einsle, O. / Chiu, H.J. / Willing, A. / Yoshida, M. / Howard, J.B. / Rees, D.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 | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 916.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 602.1 KB | Display | ![]() |
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Full document | ![]() | 880.5 KB | Display | |
Data in XML | ![]() | 156.2 KB | Display | |
Data in CIF | ![]() | 225.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | The biological assembly is a 2-alpha - 2-beta - heterotetramer crosslinked to two Fe protein dimers, i.e. half the content of the asymmetric unit. |
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Components
-Nitrogenase molybdenum-iron protein ... , 2 types, 8 molecules ACIKBDJL
#1: Protein | Mass: 55231.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 59404.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 1 types, 8 molecules EFGHMNOP
#3: Protein | Mass: 31417.045 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 20 molecules ![](data/chem/img/HCA.gif)
![](data/chem/img/CFM.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/CFM.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SF4.gif)
#4: Chemical | ChemComp-HCA / #5: Chemical | ChemComp-CFM / #6: Chemical | ChemComp-CLF / #7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-SF4 / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 8 Details: PEG 6000, NaCl, Cadaverine, Tris, pH 8.0, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 129716 / Num. obs: 105200 / % possible obs: 81.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.072 / Net I/σ(I): 13 |
Reflection shell | Resolution: 3.2→3.29 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7522 / % possible all: 70.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 225603 |
Reflection shell | *PLUS % possible obs: 70.3 % / Rmerge(I) obs: 0.666 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.22 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.33 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.44 |