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Yorodumi- PDB-7o5v: Crystal structure of holo-H44A mutant of Hydroxy ketone aldolase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o5v | ||||||
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Title | Crystal structure of holo-H44A 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 aldolase / aldol reaction / Magnesium / carbon bond formation / holo / Hydroxupyruvate | ||||||
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 / BROMIDE ION / : / HpcH/HpaI aldolase Function and homology information | ||||||
Biological species | Sphingomonas wittichii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 7o5v.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o5v.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7o5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o5v_validation.pdf.gz | 990.9 KB | Display | wwPDB validaton report |
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Full document | 7o5v_full_validation.pdf.gz | 993.1 KB | Display | |
Data in XML | 7o5v_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 7o5v_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/7o5v ftp://data.pdbj.org/pub/pdb/validation_reports/o5/7o5v | HTTPS FTP |
-Related structure data
Related structure data | 7nnkC 7nr1C 7nujC 7o5iC 7o5rC 7o5wC 7o87C 7o9rC 7obuC 8adqC 6r62S C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 26579.307 Da / Num. of mol.: 2 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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-Non-polymers , 5 types, 213 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-3PY / | #6: Water | ChemComp-HOH / | |
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-Details
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: 1.91 Å3/Da / Density % sol: 35.54 % |
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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: P14 (MX2) / Wavelength: 0.9766 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9766 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.95→53.77 Å / Num. obs: 29321 / % possible obs: 96.3 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.081 / Rrim(I) all: 0.116 / Net I/σ(I): 7.3 | |||||||||||||||||||||
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: 1.95→53.769 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.289 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.034 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: 32.704 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→53.769 Å
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Refine LS restraints |
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LS refinement shell |
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