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Yorodumi- PDB-7nnk: Crystal structure of S116A mutant of hydroxy ketone aldolase (SwH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nnk | ||||||
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Title | Crystal structure of S116A mutant of hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate | ||||||
Components | HpcH/HpaI aldolase | ||||||
Keywords | LYASE / Class II Pyruvate Aldolase / Metal Dependent / Aldol Reaction / Hydroxypyruvate / Pyruvate / Aldolase / Class II | ||||||
Function / homology | HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / catalytic activity / 3-HYDROXYPYRUVIC ACID / HpcH/HpaI aldolase Function and homology information | ||||||
Biological species | Sphingomonas wittichii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Justo, I. / Marsden, S.R. / Hanefeld, U. / Bento, I. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Substrate Induced Movement of the Metal Cofactor between Active and Resting State. Authors: Marsden, S.R. / Wijma, H.J. / Mohr, M.K.F. / Justo, I. / Hagedoorn, P.L. / Laustsen, J. / Jeffries, C.M. / Svergun, D. / Mestrom, L. / McMillan, D.G.G. / Bento, I. / Hanefeld, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nnk.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nnk.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 7nnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/7nnk ftp://data.pdbj.org/pub/pdb/validation_reports/nn/7nnk | HTTPS FTP |
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-Related structure data
Related structure data | 7nr1C 7nujC 7o5iC 7o5rC 7o5vC 7o5wC 7o87C 7o9rC 7obuC 8adqC 6r62S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26768.525 Da / Num. of mol.: 2 / Mutation: S116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) (bacteria) Strain: RW1 / DSM 6014 / JCM 10273 / Gene: Swit_5035 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VH82 #2: Chemical | ChemComp-3PY / | #3: Chemical | #4: 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: 2.05 Å3/Da / Density % sol: 40.1 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG400, HEPES, Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 17, 2020 | ||||||||||||||||||||||||
Radiation | Monochromator: Oxford-FNB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→74.39 Å / Num. obs: 38705 / % possible obs: 98.5 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.085 / Rrim(I) all: 0.132 / Net I/σ(I): 8.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R62 Resolution: 1.8→59.533 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.171 / SU B: 3.708 / SU ML: 0.111 / Average fsc free: 0.8879 / Average fsc work: 0.9052 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.138 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: 22.099 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→59.533 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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