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- PDB-8adq: Crystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8adq | ||||||
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Title | Crystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate and D-Glyceraldehyde | ||||||
![]() | HpcH/HpaI aldolase | ||||||
![]() | LYASE / Hydroxy-keto aldolase / aldol condensation / aldol cleavage / stereospecificity / TIM barrel fold | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Justo, I. / Marsden, S.R. / Hanefeld, U. / Bento, I. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.1 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nnkC ![]() 7nr1C ![]() 7nujC ![]() 7o5iC ![]() 7o5rC ![]() 7o5vC ![]() 7o5wC ![]() 7o87C ![]() 7o9rC ![]() 7obuC ![]() 6r62S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 3 molecules A![](data/chem/img/3GR.gif)
![](data/chem/img/3GR.gif)
#1: Protein | Mass: 27468.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1 Gene: Swit_5035 / Production host: ![]() ![]() |
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#3: Sugar |
-Non-polymers , 6 types, 252 molecules ![](data/chem/img/3PY.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-3PY / | ||||||||
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#4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-MG / | #6: Chemical | #7: Chemical | ChemComp-K / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.17 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.44 M-0.65 M sodium citrate 0.1 M HEPES at pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2021 |
Radiation | Monochromator: MD2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.9 Å / Num. obs: 35573 / % possible obs: 99.96 % / Redundancy: 38.5 % / Biso Wilson estimate: 29.67 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.0116 / Rrim(I) all: 0.0721 / Rsym value: 0.071 / Net I/σ(I): 30.94 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 39.9 % / Rmerge(I) obs: 2.98 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 3490 / CC1/2: 0.65 / CC star: 0.89 / Rpim(I) all: 0.48 / Rrim(I) all: 3.02 / % possible all: 99.91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6r62 Resolution: 1.6→40.9 Å / SU ML: 0.2008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2293 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: 35.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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