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Yorodumi- PDB-7ete: Crystal structure of AbHpaI-Mg-(4R)-KDGal complex, Class II aldol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ete | |||||||||
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Title | Crystal structure of AbHpaI-Mg-(4R)-KDGal complex, Class II aldolase, HpaI from Acinetobacter baumannii | |||||||||
Components | 4-hydroxy-2-oxoheptanedioate aldolase | |||||||||
Keywords | LYASE / TIM barrel / aldehyde lyase | |||||||||
Function / homology | Function and homology information 4-hydroxy-2-oxoheptanedioate aldolase / 2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity / phenylacetate catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Model details | Crystal structure of AbHpaI-Zn-pyruvate complex, a class II aldolase, HpaI from Acinetobacter baumannii | |||||||||
Authors | Watthaisong, P. / Binlaeh, A. / Jaruwat, A. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S. | |||||||||
Funding support | Thailand, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii. Authors: Watthaisong, P. / Binlaeh, A. / Jaruwat, A. / Lawan, N. / Tantipisit, J. / Jaroensuk, J. / Chuaboon, L. / Phonbuppha, J. / Tinikul, R. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ete.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ete.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ete.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/7ete ftp://data.pdbj.org/pub/pdb/validation_reports/et/7ete | HTTPS FTP |
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-Related structure data
Related structure data | 7et8SC 7et9C 7etaC 7etbC 7etcC 7etdC 7etfC 7etgC 7ethC 7etiC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28755.910 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hpaI, FD887_17235 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A5R9HKL3, 4-hydroxy-2-oxoheptanedioate aldolase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #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: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 4.6 / Details: CaCl2, MPD, Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 7, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→24.41 Å / Num. obs: 89082 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.05 / Rrim(I) all: 0.131 / Net I/σ(I): 11 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ET8 Resolution: 1.9→24.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.916 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.97 Å2 / Biso mean: 15.856 Å2 / Biso min: 4.95 Å2
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Refinement step | Cycle: final / Resolution: 1.9→24.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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