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- PDB-7etd: Crystal structure of AbHpaI-Zn-(4S)-KDGlu complex, Class II aldol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7etd | |||||||||
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Title | Crystal structure of AbHpaI-Zn-(4S)-KDGlu complex, Class II aldolase, HpaI from Acinetobacter baumannii | |||||||||
![]() | 4-hydroxy-2-oxoheptanedioate aldolase | |||||||||
![]() | LYASE / TIM barrel / aldehyde lyase | |||||||||
Function / homology | ![]() 4-hydroxy-2-oxoheptanedioate aldolase / : / phenylacetate catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
Model details | Crystal structure of AbHpaI-Zn-pyruvate complex, a class II aldolase, HpaI from Acinetobacter baumannii | |||||||||
![]() | Watthaisong, P. / Binlaeh, A. / Jaruwat, A. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171 KB | Display | ![]() |
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PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7et8SC ![]() 7et9C ![]() 7etaC ![]() 7etbC ![]() 7etcC ![]() 7eteC ![]() 7etfC ![]() 7etgC ![]() 7ethC ![]() 7etiC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28755.910 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.54 % |
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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: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 5, 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: 1.68→24.43 Å / Num. obs: 75151 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.056 / Rrim(I) all: 0.147 / Net I/σ(I): 9.5 / Num. measured all: 702036 / Scaling rejects: 682 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ET8 Resolution: 1.9→23.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.731 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.11 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.37 Å2 / Biso mean: 13.417 Å2 / Biso min: 5.25 Å2
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Refinement step | Cycle: final / Resolution: 1.9→23.58 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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