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- PDB-2bon: Structure of an Escherichia coli lipid kinase (YegS) -

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Basic information

Entry
Database: PDB / ID: 2bon
TitleStructure of an Escherichia coli lipid kinase (YegS)
ComponentsLIPID KINASE
KeywordsTRANSFERASE / DAG KINASE
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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBakali, H.M. / Johnson, K.A. / Hallberg, B.M. / Herman, M.D. / Nordlund, P.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of Yegs, a Homologue to the Mammalian Diacylglycerol Kinases, Reveals a Novel Regulatory Metal Binding Site.
Authors: Bakali, H.M. / Herman, M.D. / Johnson, K.A. / Kelly, A.A. / Wieslander, A. / Hallberg, B.M. / Nordlund, P.
History
DepositionApr 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.pdbx_dist_value / _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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPID KINASE
B: LIPID KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9104
Polymers71,8612
Non-polymers492
Water1,27971
1
A: LIPID KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9552
Polymers35,9311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIPID KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9552
Polymers35,9311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.326, 166.164, 48.474
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LIPID KINASE


Mass: 35930.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76407
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.4 Å3/Da / Density % sol: 47.4 %
Description: THE DATA ARE VERY ANISOTROPIC. DATA FOR REFINEMENT WERE SELECTED BY CALCULATING AN AVERAGE SIGMA ON F FOR EACH REFLECTION AND ALL NEIGHBORING REFLECTIONS. THUS, UP TO 27 REFLECTIONS ...Description: THE DATA ARE VERY ANISOTROPIC. DATA FOR REFINEMENT WERE SELECTED BY CALCULATING AN AVERAGE SIGMA ON F FOR EACH REFLECTION AND ALL NEIGHBORING REFLECTIONS. THUS, UP TO 27 REFLECTIONS CONTRIBUTED TO THE AVERAGE SIGMA CUTOFF VALUE FOR EACH REFLECTION. THIS AVERAGED SIGMA CUTOFF WAS SET AT 4 SIGMA RESULTING IN A DATA SET 98 PERCENT COMPLETE TO 2.7 ANGSTROMS AND 73 PERCENT COMPLETE OVERALL TO 1.9 ANGSTROMS. THE FIRST DATA SET WAS USED FOR REFINEMENT. THE SECOND DATA SET CONTAINS ALL THE OBSERVED STRUCTURE FACTORS WITH THE STATISTICS GIVEN.
Crystal growpH: 5.5
Details: 15% PEG 3350 0.1 M BIS-TRIS PH 5.5 0.2 M MGCL2 PLUS 15%PEG400 AS CRYOPROTECTANT.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939, 0.939
DetectorType: ADSC QUANTUM-4 / Detector: CCD / Date: Nov 7, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 38253 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→83.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.16 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES ARE NUMBERED ACCORDING TO THE NATIVE SEQUENCE. TLS GROUPS WERE CHOSEN BY DOMAIN. THE MAGNESIUM AND WATER ATOMS WERE ASSIGNED TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES ARE NUMBERED ACCORDING TO THE NATIVE SEQUENCE. TLS GROUPS WERE CHOSEN BY DOMAIN. THE MAGNESIUM AND WATER ATOMS WERE ASSIGNED TO TLS GROUPS BY PROXIMITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1984 5.2 %RANDOM
Rwork0.22 ---
obs0.222 36269 73.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.89 Å2
Baniso -1Baniso -2Baniso -3
1-9 Å20 Å20.32 Å2
2---4.71 Å20 Å2
3----4.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→83.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 2 71 4215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224210
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9715710
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57324.835182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84515697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2091528
X-RAY DIFFRACTIONr_chiral_restr0.1130.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023174
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21762
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22836
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8831.52800
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35824358
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13531562
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2084.51352
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 68
Rwork0.234 1394
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0162-1.1327-0.28938.87760.04152.92290.09410.2927-0.4028-0.7692-0.2978-0.00980.7423-0.22540.20370.18310.02480.0487-0.1897-0.1426-0.15323.7405-8.22145.2328
22.5098-0.0492-2.01144.58180.34834.20480.03730.1463-0.2373-0.0638-0.10340.65250.2505-0.45860.066-0.07060.0231-0.0236-0.2818-0.0374-0.3117-7.81939.973220.9034
30.2474-1.53130.02789.5821-0.89945.05280.03660.26290.2571-0.4118-0.15260.1138-0.8090.19030.1160.0215-0.01620.0244-0.17960.0962-0.1294-3.700548.862-20.3386
41.2158-0.78460.44447.0386-0.64689.1547-0.0241-0.10450.35810.2121-0.1119-0.5087-0.43060.78410.136-0.2851-0.01270.0259-0.2643-0.0154-0.31142.259231.0045-1.9529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 124
2X-RAY DIFFRACTION1A286 - 301
3X-RAY DIFFRACTION2A125 - 285
4X-RAY DIFFRACTION2A1302
5X-RAY DIFFRACTION3B5 - 124
6X-RAY DIFFRACTION3B286 - 301
7X-RAY DIFFRACTION4B125 - 285
8X-RAY DIFFRACTION4B1302

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