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- PDB-2p1r: Crystal structure of Salmonella typhimurium YegS, a putative lipi... -

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Basic information

Entry
Database: PDB / ID: 2p1r
TitleCrystal structure of Salmonella typhimurium YegS, a putative lipid kinase homologous to eukaryotic sphingosine and diacylglycerol kinases.
ComponentsLipid kinase yegS
KeywordsTRANSFERASE / YegS / diacylglycerol / kinase / lipid / ATP-binding / Magnesium / Metal-binding / ----
Function / homology
Function and homology information


lipid kinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / phospholipid biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Lipid kinase YegS / Diacylglycerol/lipid kinase / YegS/DAGK, C-terminal domain / YegS C-terminal NAD kinase beta sandwich-like domain / Tumour Suppressor Smad4 - #40 / : / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) ...Lipid kinase YegS / Diacylglycerol/lipid kinase / YegS/DAGK, C-terminal domain / YegS C-terminal NAD kinase beta sandwich-like domain / Tumour Suppressor Smad4 - #40 / : / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Probable lipid kinase YegS
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsNichols, C.E. / Lamb, H.K. / Lockyer, M. / Charles, I.G. / Pyne, S. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: Proteins: Struct.,Funct.,Genet. / Year: 2007
Title: Characterization of Salmonella typhimurium YegS, a putative lipid kinase homologous to eukaryotic sphingosine and diacylglycerol kinases
Authors: Nichols, C.E. / Lamb, H.K. / Lockyer, M. / Charles, I.G. / Pyne, S. / Hawkins, A.R. / Stammers, D.K.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: Lipid kinase yegS
B: Lipid kinase yegS
C: Lipid kinase yegS
D: Lipid kinase yegS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,06018
Polymers129,5434
Non-polymers51814
Water7,458414
1
A: Lipid kinase yegS
C: Lipid kinase yegS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0309
Polymers64,7712
Non-polymers2597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipid kinase yegS
D: Lipid kinase yegS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0309
Polymers64,7712
Non-polymers2597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.000, 70.990, 102.160
Angle α, β, γ (deg.)90.00, 118.51, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A and C form one biological dimer, Chains B and D form a second dimer.

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Components

#1: Protein
Lipid kinase yegS


Mass: 32385.705 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: yegS / Plasmid: pRF69 / Production host: Escherichia coli (E. coli) / Strain (production host): B384pLysS
References: UniProt: Q8ZNP1, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: pH 7.4, 17% PEG3350, 0.2M ammonium sulphate. VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.885596, 0.979239, 0.885596
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2004
Details: Si(111) monochromator. Mirror 1: Grazing angle 2.8 mrad, vertical focusing. Mirror 2: vertical and horizontal focusing.
RadiationMonochromator: Si(111) monochromator. / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8855961
20.9792391
ReflectionResolution: 2.5→30 Å / Num. all: 46970 / Num. obs: 45865 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.2 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.46
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.74 / Num. unique all: 3506 / % possible all: 83.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1492706.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1.8 / ESU R: 0.746 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4620 10.1 %RANDOM
Rwork0.206 ---
obs-45843 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4313 Å2 / ksol: 0.303722 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.88 Å20 Å23.67 Å2
2---2.7 Å20 Å2
3---8.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8616 0 14 414 9044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.41 380 9.8 %
Rwork0.37 3506 -
obs--83.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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