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- PDB-4uyo: Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystat... -

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Basic information

Entry
Database: PDB / ID: 4uyo
TitleStructure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18 angstrom resolution
ComponentsDIACYLGLYCEROL KINASE-DELTA 7
KeywordsTRANSFERASE / 7.9 MAG / IN MESO CRYSTALLIZATION / LIPID CUBIC PHASE / LIPIDIC CUBIC PHASE / LIPID MESOPHASE / LIPIDIC MESOPHASE / MEMBRANE PROTEIN / MICROCRYSTALS / MONOACYLGLYCEROL / ROOM TEMPERATURE CRYSTALLOGRAPHY / SERIAL FEMTOSECOND CRYSTALLOGRAPHY / X-RAY FREE-ELECTRON LASER
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #3610 / DAGK family / Diacylglycerol kinase, prokaryotic / Diacylglycerol kinase (DAGK) superfamily / Prokaryotic diacylglycerol kinase / Prokaryotic diacylglycerol kinase signature. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K12 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLi, D. / Howe, N. / Other, O. / Caffrey, M.
CitationJournal: Nat.Commun. / Year: 2015
Title: Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase.
Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / ...Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / Weierstall, U. / Zatsepin, N.A. / Cherezov, V. / Liu, W. / Bandaru, S. / English, N.J. / Gati, C. / Barty, A. / Yefanov, O. / Chapman, H.N. / Diederichs, K. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Marvin Seibert, M. / Caffrey, M.
History
DepositionSep 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 1.3Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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: DIACYLGLYCEROL KINASE-DELTA 7
B: DIACYLGLYCEROL KINASE-DELTA 7
C: DIACYLGLYCEROL KINASE-DELTA 7
D: DIACYLGLYCEROL KINASE-DELTA 7
E: DIACYLGLYCEROL KINASE-DELTA 7
F: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,43817
Polymers85,2276
Non-polymers3,21111
Water1,53185
1
A: DIACYLGLYCEROL KINASE-DELTA 7
B: DIACYLGLYCEROL KINASE-DELTA 7
C: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2568
Polymers42,6133
Non-polymers1,6425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DIACYLGLYCEROL KINASE-DELTA 7
E: DIACYLGLYCEROL KINASE-DELTA 7
F: DIACYLGLYCEROL KINASE-DELTA 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1829
Polymers42,6133
Non-polymers1,5686
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.300, 91.800, 141.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
DIACYLGLYCEROL KINASE-DELTA 7 / DAGK / DIGLYCERIDE KINASE / DGK / DIACYLGLYCEROL KINASE-DELTA7


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K12 (bacteria) / Plasmid: PTRCHISB-DGKA-DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Non-polymers , 5 types, 96 molecules

#2: Chemical
ChemComp-79N / (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H36O4
#3: Chemical
ChemComp-79M / (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / [(2R)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H36O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 140440

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 % / Description: R SPLIT (I) 0.07, R SPLIT FOR SHELL (I) 2.38
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: 0.2 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 20 DEGREES CELCIUS WITH THE 7. ...Details: 0.2 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 20 DEGREES CELCIUS WITH THE 7.9 MONOACYLGLYCEROL (7.9 MAG) AS THE HOSTING LIPID.CRYSTALLIZATION WAS SET UP BY INCUBATING 20 MICROLITERS OF LIPID CUBIC PHASE WITH 400 MICROLITERS OF PRECIPITANT SOLUTION IN COUPLED SYRINGES.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.302 / Wavelength: 1.302 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Mar 25, 2013
RadiationMonochromator: K-B MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.302 Å / Relative weight: 1
ReflectionResolution: 2.18→40.5 Å / Num. obs: 54058 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 3466 % / Biso Wilson estimate: 71.31 Å2 / Net I/σ(I): 19
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 3519 % / Mean I/σ(I) obs: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZE3

3ze3


Resolution: 2.18→40.013 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 28.73 / Stereochemistry target values: ML
Details: THERE ARE SIX NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2362 2583 5 %
Rwork0.2076 --
obs0.209 51797 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.42 Å2
Refinement stepCycle: LAST / Resolution: 2.18→40.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 221 85 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085244
X-RAY DIFFRACTIONf_angle_d0.9497132
X-RAY DIFFRACTIONf_dihedral_angle_d13.9631927
X-RAY DIFFRACTIONf_chiral_restr0.057855
X-RAY DIFFRACTIONf_plane_restr0.003873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.22190.38671450.37722591X-RAY DIFFRACTION96
2.2219-2.26730.34151360.35632676X-RAY DIFFRACTION99
2.2673-2.31660.38811500.34462681X-RAY DIFFRACTION100
2.3166-2.37050.39251260.33292737X-RAY DIFFRACTION100
2.3705-2.42970.36231580.31262700X-RAY DIFFRACTION100
2.4297-2.49540.33191510.29712686X-RAY DIFFRACTION100
2.4954-2.56880.3231600.26932707X-RAY DIFFRACTION100
2.5688-2.65170.25791470.23852694X-RAY DIFFRACTION100
2.6517-2.74650.27371300.2172715X-RAY DIFFRACTION100
2.7465-2.85640.26891500.2012723X-RAY DIFFRACTION100
2.8564-2.98640.24261410.19322738X-RAY DIFFRACTION100
2.9864-3.14380.25981460.18812760X-RAY DIFFRACTION100
3.1438-3.34060.2651450.19622722X-RAY DIFFRACTION100
3.3406-3.59840.23671290.18682783X-RAY DIFFRACTION100
3.5984-3.96030.22871310.17712771X-RAY DIFFRACTION100
3.9603-4.53260.16311330.15482792X-RAY DIFFRACTION100
4.5326-5.7080.23471610.21632798X-RAY DIFFRACTION100
5.708-40.01970.23441440.232940X-RAY DIFFRACTION99

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