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Yorodumi- PDB-7o5i: Crystal structure of apo-SwHKA (Hydroxy ketone aldolase) from Sph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o5i | ||||||
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Title | Crystal structure of apo-SwHKA (Hydroxy ketone aldolase) from Sphingomonas wittichii RW1 | ||||||
Components | HpcH/HpaI aldolase | ||||||
Keywords | LYASE / Class II pyruvate aldolase / Metal dependent aldolase / aldol reaction / carbon bond formation / apo | ||||||
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 / BROMIDE ION / : / DI(HYDROXYETHYL)ETHER / HpcH/HpaI aldolase Function and homology information | ||||||
Biological species | Sphingomonas wittichii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Laustsen, J. / 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 | 7o5i.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o5i.ent.gz | 135.3 KB | Display | PDB format |
PDBx/mmJSON format | 7o5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/7o5i ftp://data.pdbj.org/pub/pdb/validation_reports/o5/7o5i | HTTPS FTP |
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-Related structure data
Related structure data | 7nnkC 7nr1C 7nujC 7o5rC 7o5vC 7o5wC 7o87C 7o9rC 7obuC 8adqC 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: 26922.670 Da / Num. of mol.: 1 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 | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, Sodium Citrate |
-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: Mar 26, 2021 | |||||||||||||||||||||
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: 1.35→116.38 Å / Num. obs: 59487 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 16.95 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.025 / Rrim(I) all: 0.114 / Net I/σ(I): 12.9 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→52.04 Å / SU ML: 0.1101 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.8811 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→52.04 Å
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Refine LS restraints |
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LS refinement shell |
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