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- PDB-4uqp: High-resolution structure of the D. fructosovorans NiFe-hydrogena... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uqp | ||||||
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Title | High-resolution structure of the D. fructosovorans NiFe-hydrogenase L122A mutant after exposure to air | ||||||
![]() | (PERIPLASMIC [NIFE] HYDROGENASE ...) x 2 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Volbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / DeLacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C. | ||||||
![]() | ![]() Title: Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures for the Elusive Unready Oxidized States. Authors: Volbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / De Lacey, A.L. / Liebgott, P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C. #1: ![]() Title: Structural Differences between the Ready and Unready Oxidized States of [Nife] Hydrogenases. Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P.J. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.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 | ![]() | 697.3 KB | Display | ![]() |
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PDB format | ![]() | 574.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Components
-PERIPLASMIC [NIFE] HYDROGENASE ... , 2 types, 4 molecules ABQR
#1: Protein | Mass: 28418.389 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 50-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Protein | Mass: 61190.777 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 10 types, 1712 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SOT.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SOT.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ChemComp-SOT / | #7: Chemical | ChemComp-H2S / | ![]() #8: Chemical | #9: Chemical | ![]() #10: Chemical | #11: Chemical | ![]() #12: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | L122A MUTATION AND N-TERMINAL STREP-TAG IN LARGE SUBUNIT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 6.1 Details: VAPOR DIFFUSION, ANAEROBIC GROWTH, 298 K, PEG 6000, MES, HEPES, CRYSTAL EXPOSED 3 DAYS TO AIR, PH 6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.42→44.1 Å / Num. obs: 264128 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.59 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.48 |
Reflection shell | Resolution: 1.42→1.5 Å / Redundancy: 2.83 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.4 / % possible all: 86.4 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→30 Å
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Refine LS restraints |
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