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Yorodumi- PDB-1qgu: NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, DITHIONITE-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qgu | ||||||
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Title | NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, DITHIONITE-REDUCED STATE | ||||||
Components | (PROTEIN (NITROGENASE MOLYBDENUM IRON ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / BIOLOGICAL NITROGEN FIXATION / NITROGEN METABOLISM / MOLYBDOENZYMES / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mayer, S.M. / Lawson, D.M. / Gormal, C.A. / Roe, S.M. / Smith, B.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qgu.cif.gz | 470.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qgu.ent.gz | 371.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qgu_validation.pdf.gz | 528.5 KB | Display | wwPDB validaton report |
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Full document | 1qgu_full_validation.pdf.gz | 556 KB | Display | |
Data in XML | 1qgu_validation.xml.gz | 98 KB | Display | |
Data in CIF | 1qgu_validation.cif.gz | 152.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qgu ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qgu | HTTPS FTP |
-Related structure data
Related structure data | 1qh1C 1qh8C 1min C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Klebsiella pneumoniae (bacteria) / Cellular location: CYTOPLASM / Variant: WILD-TYPE / Strain: M5A1 / References: UniProt: P00466, nitrogenase #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) Klebsiella pneumoniae (bacteria) / Cellular location: CYTOPLASM / Variant: WILD-TYPE / Strain: M5A1 / References: UniProt: P09772, nitrogenase |
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-Non-polymers , 7 types, 2800 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: liquid diffusion / 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 PRIOR TO DATA COLLECTION THE CRYSTAL WAS INCUBATED FOR 24 HOURS IN CRYOPROTECTANT (MOTHER LIQUOR WITH 25% ETHYLENE GLYCOL) CONTAINING 10 MM SODIUM DITHIONITE (A REDUCTANT). | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.872 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: RH COATED SI MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.872 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 260359 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 5.8 / % possible all: 96.4 |
Reflection shell | *PLUS % possible obs: 96.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: 17.79 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: 0.156 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |