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Yorodumi- PDB-6d4c: Crystal structure of Candida boidinii formate dehydrogenase V123G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d4c | ||||||
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Title | Crystal structure of Candida boidinii formate dehydrogenase V123G mutant complexed with NAD+ and azide | ||||||
Components | Formate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ternary complex | ||||||
Function / homology | Function and homology information formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Candida boidinii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Guo, Q. / Ye, H. / Gakhar, L. / Cheatum, C.M. / Kohen, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Catalysis / Year: 2019 Title: Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase Authors: Pagano, P.L. / Guo, Q. / Ranasinghe, C. / Schroeder, E. / Robben, K. / Hase, F. / Ye, H. / Wickersham, K. / Aspuru-Guzik, A. / Major, D.T. / Gakhar, L. / Kohen, A. / Cheatum, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d4c.cif.gz | 302.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d4c.ent.gz | 246.4 KB | Display | PDB format |
PDBx/mmJSON format | 6d4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/6d4c ftp://data.pdbj.org/pub/pdb/validation_reports/d4/6d4c | HTTPS FTP |
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-Related structure data
Related structure data | 6d4bC 5dn9S S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 40322.891 Da / Num. of mol.: 2 / Mutation: V123G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida boidinii (fungus) / Gene: FDH Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0A1EQY0, formate dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.28 Å3/Da / Density % sol: 46.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 25% PEG 3000, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→45.985 Å / Num. obs: 123164 / % possible obs: 91.39 % / Redundancy: 3.7 % / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.45→1.47 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DN9 Resolution: 1.45→45.985 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 19.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→45.985 Å
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Refine LS restraints |
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LS refinement shell |
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