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Yorodumi- PDB-7qnh: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qnh | ||||||
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Title | CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NADH, AND GLYCEROL | ||||||
Components | Lactaldehyde reductase | ||||||
Keywords | OXIDOREDUCTASE / FucO / NADH / Dehydrogenase / aldehyde reductase | ||||||
Function / homology | Function and homology information lactaldehyde reductase / R-lactaldehyde reductase activity / S-lactaldehyde reductase activity / fucose catabolic process / alcohol dehydrogenase (NAD+) activity / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Iucrj / Year: 2023 Title: Crystal structures and kinetic studies of a laboratory evolved aldehyde reductase explain the dramatic shift of its new substrate specificity. Authors: Sridhar, S. / Zavarise, A. / Kiema, T.R. / Dalwani, S. / Eriksson, T. / Hajee, Y. / Reddy Enugala, T. / Wierenga, R.K. / Widersten, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qnh.cif.gz | 388.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qnh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/7qnh ftp://data.pdbj.org/pub/pdb/validation_reports/qn/7qnh | HTTPS FTP |
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-Related structure data
Related structure data | 7qlgC 7qlqC 7qlsC 1rrmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 3 - 385 / Label seq-ID: 3 - 385
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 41464.230 Da / Num. of mol.: 2 / Mutation: N151G,L259V,S315G Source method: isolated from a genetically manipulated source Details: M M A N R M I L N E T A W F G R G A V G A L T D E V K R R G Y Q K A L I V T D K T L V Q C G V V A K V T D K M D A A G L A W A I Y D G V V P N P T I T V V K E G L G V F Q N S G A D Y L I A I ...Details: M M A N R M I L N E T A W F G R G A V G A L T D E V K R R G Y Q K A L I V T D K T L V Q C G V V A K V T D K M D A A G L A W A I Y D G V V P N P T I T V V K E G L G V F Q N S G A D Y L I A I G G G T P Q D T C K A I G I I S N N P E F A D V R S L E G L S P T N K P S V P I L A I P T T A G T A A E V T I G Y V I T D E E K R R K F V C V D P H D I P Q V A F I D A D M M D G M P P A L K A A T G V D A L T H A I E G Y I T R G A W A L T D A L H I K A I E I I A G A L R G S V A G D K D A G E E M A L G Q Y V A G M G F S N V G V G L V H G M A H P L G A F Y N T P H G V A N A I L L P H V M R Y N A D F T G E K Y R D I A R V M G V K V E G M S L E E A R N A A V E A V F A L N R D V G N P P H L R D V G V R K E D I P A L A Q A A L D D V C T G G N P R E A T L E D I V E L Y H T A W T S H H H H H Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: fucO, Z4116, ECs3659 / Production host: Escherichia coli (E. coli) / Variant (production host): XL1-Blue / References: UniProt: P0A9S2, lactaldehyde reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 50.64 mM Sodium acetate trihydrate, pH 4.5; 15 % (w/v) PEG 3350; 200 mM sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Apr 21, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→51.883 Å / Num. obs: 39813 / % possible obs: 99.8 % / Redundancy: 1.92 % / Biso Wilson estimate: 14.11 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.082 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 1.94 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3466 / CC1/2: 0.85 / Rpim(I) all: 0.292 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RRM Resolution: 2.2→51.883 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: FREE R-VALUE / ESU R: 0.306 / ESU R Free: 0.206 Details: Hydrogens have been added in their riding positions
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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: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.805 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→51.883 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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