+Open data
-Basic information
Entry | Database: PDB / ID: 3mau | ||||||
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Title | Crystal structure of StSPL in complex with phosphoethanolamine | ||||||
Components | sphingosine-1-phosphate lyaseSGPL1 | ||||||
Keywords | LYASE / carboxy-lyase activity / pyridoxyl phosphate | ||||||
Function / homology | Function and homology information aromatic-L-amino-acid decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Symbiobacterium thermophilum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Bourquin, F. / Grutter, M.G. / Capitani, G. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structure and Function of Sphingosine-1-Phosphate Lyase, a Key Enzyme of Sphingolipid Metabolism. Authors: Bourquin, F. / Riezman, H. / Capitani, G. / Grutter, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mau.cif.gz | 342.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mau.ent.gz | 279.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3mau ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3mau | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 57 - 507 / Label seq-ID: 58 - 508
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-Components
#1: Protein | Mass: 55572.996 Da / Num. of mol.: 4 / Mutation: K311A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Symbiobacterium thermophilum (bacteria) Gene: STH1274 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: Q67PY4, sphinganine-1-phosphate aldolase #2: Chemical | ChemComp-PLR / ( | #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: PEG 5000 MME 17%, 0.15 M KSCN, 0.1 M Tris(HOAc) pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2007 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.9 Å / Num. obs: 48405 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 63.916 Å2 / Rsym value: 0.126 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 2.8 / Num. measured obs: 27013 / Num. unique obs: 4383 / Rsym value: 0.579 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NON-DEPOSITED STRUCTURE OF STSPL K311A (DIMERIC MODEL) WITHOUT PHOSPHOETHANOLAMINE BOUND Resolution: 2.9→29.895 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.805 / SU ML: 0.34 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.33 / 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 / Bsol: 16.325 Å2 / ksol: 0.269 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.54 Å2 / Biso mean: 71.046 Å2 / Biso min: 47.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→29.895 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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