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Yorodumi- PDB-8adq: Crystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) from... -
+Open data
-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 | ||||||
Components | HpcH/HpaI aldolase | ||||||
Keywords | LYASE / Hydroxy-keto aldolase / aldol condensation / aldol cleavage / stereospecificity / TIM barrel fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhizorhabdus wittichii RW1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Justo, I. / Marsden, S.R. / Hanefeld, U. / Bento, I. | ||||||
Funding support | 1items
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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 | 8adq.cif.gz | 189.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8adq.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 8adq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/8adq ftp://data.pdbj.org/pub/pdb/validation_reports/ad/8adq | HTTPS FTP |
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-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 (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
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 27468.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizorhabdus wittichii RW1 (bacteria) Strain: DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1 Gene: Swit_5035 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VH82 |
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#3: Sugar |
-Non-polymers , 6 types, 252 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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