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Yorodumi- PDB-5jsp: New Mechanistic Insight from Substrate and Product Bound Structur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jsp | ||||||
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Title | New Mechanistic Insight from Substrate and Product Bound Structures of the Metal-dependent Dimethylsulfoniopropionate Lyase DddQ | ||||||
Components | Dimethlysulfonioproprionate lyase DddQ | ||||||
Keywords | LYASE / dimethylsulfoniopropionate / cupin / metalloenzyme | ||||||
Function / homology | Function and homology information dimethylpropiothetin dethiomethylase / dimethylpropiothetin dethiomethylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Ruegeria lacuscaerulensis | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Brummett, A.E. / Dey, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. Authors: Brummett, A.E. / Dey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jsp.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jsp.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/5jsp ftp://data.pdbj.org/pub/pdb/validation_reports/js/5jsp | HTTPS FTP |
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-Related structure data
Related structure data | 5jsoC 5jsrC 4la2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22395.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruegeria lacuscaerulensis (strain DSM 11314 / KCTC 2953 / ITI-1157) (bacteria) Strain: DSM 11314 / KCTC 2953 / ITI-1157 / Gene: dddQ, SL1157_0332 / Production host: Escherichia coli (E. coli) References: UniProt: D0CY60, dimethylpropiothetin dethiomethylase |
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-Non-polymers , 6 types, 307 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris propane pH 6.5, 0.2 M NaBr, 21% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→38.769 Å / Num. all: 20992 / Num. obs: 20992 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 16.94 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Rsym value: 0.082 / Net I/av σ(I): 8.47 / Net I/σ(I): 17 / Num. measured all: 150584 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LA2 Resolution: 2.2→38.769 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.53 / Stereochemistry target values: ML
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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 max: 52.27 Å2 / Biso mean: 16.1374 Å2 / Biso min: 4.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→38.769 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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