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- PDB-3mbb: Crystal structure of StSPL - apo form, after treatment with semic... -

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Basic information

Entry
Database: PDB / ID: 3mbb
TitleCrystal structure of StSPL - apo form, after treatment with semicarbazide
ComponentsPutative sphingosine-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: 2.051 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 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Derived calculations
Revision 1.3Apr 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sphingosine-1-phosphate lyase
B: Putative sphingosine-1-phosphate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7578
Polymers111,2922
Non-polymers4656
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-138 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.650, 126.990, 136.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative sphingosine-1-phosphate lyase


Mass: 55646.113 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.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG 5000 MME 17%, 0.15 M KSCN, 0.1 M Tris(HOAc) pH 8.6, 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: Jun 25, 2008 / 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: 2.05→30 Å / Num. obs: 63157 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.079 / Net I/σ(I): 16.4
Reflection shellResolution: 2.05→2.2 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.431 / % possible all: 95

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.5_2refinement
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: 2.051→29.41 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.23 / Isotropic thermal model: ISOTROPIC / σ(F): 1.36 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 875 1.39 %
Rwork0.1811 --
obs0.1816 63122 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.028 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4474 Å20 Å20 Å2
2--0.3455 Å20 Å2
3---2.1019 Å2
Refinement stepCycle: LAST / Resolution: 2.051→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6838 0 25 577 7440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077098
X-RAY DIFFRACTIONf_angle_d1.0889711
X-RAY DIFFRACTIONf_dihedral_angle_d16.592482
X-RAY DIFFRACTIONf_chiral_restr0.0731054
X-RAY DIFFRACTIONf_plane_restr0.0121275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.051-2.17950.25061370.21139819X-RAY DIFFRACTION95
2.1795-2.34770.26351430.186710305X-RAY DIFFRACTION100
2.3477-2.58390.22671470.181710393X-RAY DIFFRACTION100
2.5839-2.95750.2121480.182710418X-RAY DIFFRACTION100
2.9575-3.72490.22971480.177610487X-RAY DIFFRACTION100
3.7249-29.41350.18991520.171110825X-RAY DIFFRACTION100

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