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- PDB-3mad: Crystal structure of StSPL (symmetric form) -

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Basic information

Entry
Database: PDB / ID: 3mad
TitleCrystal structure of StSPL (symmetric form)
ComponentsSphingosine-1-phosphate lyase
KeywordsLYASE / carboxy-lyase activity / Pyridoxal phosphate
Function / homology
Function and homology information


sphinganine-1-phosphate aldolase activity / aromatic-L-amino-acid decarboxylase activity / sphingolipid catabolic process / carboxylic acid metabolic process / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
Helix Hairpins - #2150 / : / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Helix Hairpins / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Helix non-globular ...Helix Hairpins - #2150 / : / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Helix Hairpins / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Helix non-globular / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Special / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Putative sphingosine-1-phosphate lyase
Similarity search - Component
Biological speciesSymbiobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBourquin, F. / Grutter, M.G. / Capitani, G.
CitationJournal: 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
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingosine-1-phosphate lyase
B: Sphingosine-1-phosphate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9084
Polymers111,7182
Non-polymers1902
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-119 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.630, 126.760, 137.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sphingosine-1-phosphate lyase


Mass: 55859.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Symbiobacterium thermophilum (bacteria)
Gene: STH1274 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q67PY4, sphinganine-1-phosphate aldolase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG 5000 MME 16%, 0.15 M KSCN, 0.1 M Tris(HOAc) pH 8.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2007 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.5 Å / Num. obs: 67856 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 34.403 Å2 / Rsym value: 0.092 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 2.5 / Num. measured obs: 40409 / Num. unique obs: 9097 / Rsym value: 0.603 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.4_29refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Non-deposited but refined structure of dimeric StSPL K311A

Resolution: 2→29.451 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.788 / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.247 950 1.4 %RANDOM
Rwork0.21 ---
obs0.211 67794 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.882 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 105.28 Å2 / Biso mean: 29.136 Å2 / Biso min: 13.66 Å2
Baniso -1Baniso -2Baniso -3
1--6.899 Å20 Å20 Å2
2--1.127 Å20 Å2
3---5.772 Å2
Refinement stepCycle: LAST / Resolution: 2→29.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6866 0 10 350 7226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057118
X-RAY DIFFRACTIONf_angle_d0.9779740
X-RAY DIFFRACTIONf_chiral_restr0.0641058
X-RAY DIFFRACTIONf_plane_restr0.0041276
X-RAY DIFFRACTIONf_dihedral_angle_d15.7052489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.1050.2991330.2579403953699
2.105-2.2370.2871340.2399399953399
2.237-2.410.3011340.2239411954598
2.41-2.6520.2961350.2119506964199
2.652-3.0360.2521360.2099571970799
3.036-3.8230.2471370.1949663980099
3.823-29.4540.1961410.19798911003298

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