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- PDB-3maf: Crystal structure of StSPL (asymmetric form) -

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Basic information

Entry
Database: PDB / ID: 3maf
TitleCrystal structure of StSPL (asymmetric form)
Components(sphingosine-1-phosphate lyase) x 2
KeywordsLYASE / Carboxy-lyase activity / Pyridoxal phosphate
Function / homology
Function and homology information


sphinganine-1-phosphate aldolase activity / aromatic-L-amino-acid decarboxylase activity / aspartate 1-decarboxylase activity / sphingolipid catabolic process / carboxylic acid metabolic process / coenzyme A biosynthetic 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 / Pyridoxal phosphate-dependent transferase, small domain ...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 / molecular replacement / Resolution: 2.971 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 1.2Sep 6, 2023Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)112,3174
Polymers112,1872
Non-polymers1302
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-97 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.190, 84.900, 131.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEALAALAchain A and (resseq 64:89 or resseq 102:105 or resseq...AA64 - 8969 - 94
12GLYGLYTYRTYRchain A and (resseq 64:89 or resseq 102:105 or resseq...AA102 - 105107 - 110
13ASPASPLEULEUchain A and (resseq 64:89 or resseq 102:105 or resseq...AA108 - 121113 - 126
14HISHISTHRTHRchain A and (resseq 64:89 or resseq 102:105 or resseq...AA129 - 309134 - 314
15GLYGLYGLYGLYchain A and (resseq 64:89 or resseq 102:105 or resseq...AA313 - 352318 - 357
16PROPROARGARGchain A and (resseq 64:89 or resseq 102:105 or resseq...AA355 - 393360 - 398
17LYSLYSPROPROchain A and (resseq 64:89 or resseq 102:105 or resseq...AA399 - 472404 - 477
21PHEPHEALAALAchain B and (resseq 64:89 or resseq 102:105 or resseq...BB64 - 8969 - 94
22GLYGLYTYRTYRchain B and (resseq 64:89 or resseq 102:105 or resseq...BB102 - 105107 - 110
23ASPASPLEULEUchain B and (resseq 64:89 or resseq 102:105 or resseq...BB108 - 121113 - 126
24HISHISTHRTHRchain B and (resseq 64:89 or resseq 102:105 or resseq...BB129 - 309134 - 314
25GLYGLYGLYGLYchain B and (resseq 64:89 or resseq 102:105 or resseq...BB313 - 352318 - 357
26PROPROARGARGchain B and (resseq 64:89 or resseq 102:105 or resseq...BB355 - 393360 - 398
27LYSLYSPROPROchain B and (resseq 64:89 or resseq 102:105 or resseq...BB399 - 472404 - 477

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Components

#1: Protein sphingosine-1-phosphate lyase


Mass: 56207.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LLP at residue 311
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: Protein sphingosine-1-phosphate lyase


Mass: 55979.438 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: PEG 2000 MME 25%, 0.2 M MgCl2, 0.1 M Tris(HOAc) pH 8.3, 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2006 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN(2) 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: 2.97→30 Å / Num. obs: 19779 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 36.08 Å2 / Rsym value: 0.111 / Net I/σ(I): 13.7
Reflection shellResolution: 2.97→3.1 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.3 / Num. measured obs: 9865 / Num. unique obs: 2205 / Rsym value: 0.442 / % possible all: 92.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.4_29refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DGK

2dgk


Resolution: 2.971→27.665 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.774 / SU ML: 0.4 / σ(F): 1.99 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 988 5 %
Rwork0.2 18780 -
obs0.203 19768 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.149 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 99.57 Å2 / Biso mean: 32.587 Å2 / Biso min: 7.06 Å2
Baniso -1Baniso -2Baniso -3
1--4.162 Å2-0 Å20 Å2
2---8.538 Å20 Å2
3---12.7 Å2
Refinement stepCycle: LAST / Resolution: 2.971→27.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6347 0 6 126 6479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066528
X-RAY DIFFRACTIONf_angle_d0.9738915
X-RAY DIFFRACTIONf_chiral_restr0.06980
X-RAY DIFFRACTIONf_plane_restr0.0051159
X-RAY DIFFRACTIONf_dihedral_angle_d16.1372266
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2850X-RAY DIFFRACTIONPOSITIONAL0.054
12B2850X-RAY DIFFRACTIONPOSITIONAL0.054
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 (%)
2.971-3.1270.3991320.3362516264894
3.127-3.3230.3171400.23726542794100
3.323-3.5790.2911400.21326672807100
3.579-3.9380.2861410.17926792820100
3.938-4.5060.2031420.15727042846100
4.506-5.6690.2361450.16527382883100
5.669-27.6660.2271480.192822297099

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