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Yorodumi- PDB-4ucx: Structure of the T18G small subunit mutant of D. fructosovorans N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ucx | ||||||
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Title | Structure of the T18G small subunit mutant of D. fructosovorans NiFe- hydrogenase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NIFE-HYDROGENASE / T18G MUTANT | ||||||
Function / homology | Function and homology information cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO FRUCTOSIVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Abou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Guttierez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / deLacey, A.L. / Leger, C. / Volbeda, A. ...Abou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Guttierez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / deLacey, A.L. / Leger, C. / Volbeda, A. / Burlat, B. / Dementin, S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2015 Title: A threonine stabilizes the NiC and NiR catalytic intermediates of [NiFe]-hydrogenase. Authors: Abou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Gutierrez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / De Lacey, A.L. / Leger, C. / Volbeda, A. / Burlat, B. / Dementin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ucx.cif.gz | 937.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ucx.ent.gz | 778.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ucx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/4ucx ftp://data.pdbj.org/pub/pdb/validation_reports/uc/4ucx | HTTPS FTP |
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-Related structure data
Related structure data | 4ucqC 4ucwC 1yqwS 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 2 types, 6 molecules ABCQRS
#1: Protein | Mass: 28303.260 Da / Num. of mol.: 3 / Fragment: RESIDUES 51-314 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS (bacteria) Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) / References: UniProt: P18187, cytochrome-c3 hydrogenase #2: Protein | Mass: 61200.785 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-549 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS (bacteria) Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria) / References: UniProt: P18188, cytochrome-c3 hydrogenase |
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-Non-polymers , 7 types, 634 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-MG / #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | T18G MUTANT N-TERMINAL STREP TAG |
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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: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: VAPOR DIFFUSION, PH 6.0, 293 K, PEG 6000, MES, IN A GLOVEBOX |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 160613 / % possible obs: 99.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.95→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YQW Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.054 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.912 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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