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- PDB-1qh8: NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, AS-CRYSTALLI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qh8 | ||||||
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Title | NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, AS-CRYSTALLIZED (MIXED OXIDATION) STATE | ||||||
![]() | (PROTEIN (NITROGENASE MOLYBDENUM IRON ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / BIOLOGICAL NITROGEN FIXATION / NITROGEN METABOLISM / MOLYBDOENZYMES / ELECTRON TRANSFER | ||||||
Function / homology | ![]() molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mayer, S.M. / Lawson, D.M. / Gormal, C.A. / Roe, S.M. / Smith, B.E. | ||||||
![]() | ![]() Title: New insights into structure-function relationships in nitrogenase: A 1.6 A resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein. Authors: Mayer, S.M. / Lawson, D.M. / Gormal, C.A. / Roe, S.M. / Smith, B.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 473.4 KB | Display | ![]() |
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PDB format | ![]() | 373.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 524.6 KB | Display | ![]() |
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Full document | ![]() | 550.8 KB | Display | |
Data in XML | ![]() | 99.4 KB | Display | |
Data in CIF | ![]() | 155 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qguC ![]() 1qh1C ![]() 1min 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-PROTEIN (NITROGENASE MOLYBDENUM IRON ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 53632.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ALSO KNOWN AS KLEBSIELLA PNEUMONIAE OXYTOCA. / Source: (natural) ![]() #2: Protein | Mass: 58338.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ALSO KNOWN AS KLEBSIELLA PNEUMONIAE OXYTOCA. / Source: (natural) ![]() |
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-Non-polymers , 7 types, 2872 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HCA.gif)
![](data/chem/img/CFM.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HCA.gif)
![](data/chem/img/CFM.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: CRYSTALLIZED ANAEROBICALLY USING LIQUID-LIQUID DIFFUSION TECHNIQUE. FINAL CONCENTRATIONS AFTER EQUILIBRATION WERE: 7% (W/V) PEG 6000, 0.4 - 0.6 M MGCL2, 50 MM TRIS-HCL PH 8, 3.3 MG/ML ...Details: CRYSTALLIZED ANAEROBICALLY USING LIQUID-LIQUID DIFFUSION TECHNIQUE. FINAL CONCENTRATIONS AFTER EQUILIBRATION WERE: 7% (W/V) PEG 6000, 0.4 - 0.6 M MGCL2, 50 MM TRIS-HCL PH 8, 3.3 MG/ML PROTEIN., pH 8.0, temperature 100K PRIOR TO DATA COLLECTION THE CRYSTAL WAS TRANSIENTLY SOAKED IN CRYOPROTECTANT (MOTHER LIQUOR WITH 25% ETHYLENE GLYCOL) CONTAINING 2 MM SODIUM DITHIONITE (A REDUCTANT). | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8 / Method: liquid diffusion | ||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 265023 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 14.83 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.82 / % possible all: 84.7 |
Reflection shell | *PLUS % possible obs: 84.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MIN ![]() 1min Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: TOWARDS THE END OF REFINEMENT ALL RESTRAINTS WITHIN THE HETEROGENS HCA, CFM, AND CLF WERE EXPLICITLY TURNED OFF. IN ADDITION, THE BONDS BETWEEN THESE HETEROGENS AND THE PROTEIN (SEE ...Details: TOWARDS THE END OF REFINEMENT ALL RESTRAINTS WITHIN THE HETEROGENS HCA, CFM, AND CLF WERE EXPLICITLY TURNED OFF. IN ADDITION, THE BONDS BETWEEN THESE HETEROGENS AND THE PROTEIN (SEE CONNECTIVITY SECTION) WERE NOT RESTRAINED.
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Displacement parameters | Biso mean: 17.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.155 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |