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- PDB-3ze3: Crystal structure of the integral membrane diacylglycerol kinase ... -

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Basic information

Entry
Database: PDB / ID: 3ze3
TitleCrystal structure of the integral membrane diacylglycerol kinase - delta7
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / LIPID METABOLISM / IN MESO CRYSTALLISATION / LIPID CUBIC PHASE / LIPIDIC MESOPHASE / THERMOSTABLE MUTANT / MONOACYLGLYCEROL / 7.8 MAG
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
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / ACETATE ION / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsLi, D. / Pye, V.E. / Lyons, J.A. / Vogeley, L. / Aragao, D. / Caffrey, M.
CitationJournal: Nature / Year: 2013
Title: Crystal Structure of the Integral Membrane Diacylglycerol Kinase.
Authors: Li, D. / Lyons, J.A. / Pye, V.E. / Vogeley, L. / Aragao, D. / Kenyon, C.P. / Shah, S.T.A. / Doherty, C. / Aherne, M. / Caffrey, M.
History
DepositionDec 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Mar 29, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,67424
Polymers85,2276
Non-polymers4,44818
Water3,369187
1
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,23112
Polymers42,6133
Non-polymers1,6179
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-142.9 kcal/mol
Surface area13990 Å2
MethodPISA
2
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,44312
Polymers42,6133
Non-polymers2,8309
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-80 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.060, 91.540, 143.650
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 / DAGK / DIGLYCERIDE KINASE / DGK


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria)
Description: THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N- TERMINUS. SITE-DIRECTED ...Description: THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N- TERMINUS. SITE-DIRECTED MUTATIONS WERE MADE USING PCR.
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 , 7 types, 205 molecules

#2: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O4
#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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78M): ALSO CONTAINS THE R-ISOMER OF THIS LIPID
Sequence detailsTHE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE ...THE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS SEVEN MUTATIONS. THEY ARE A41C, C46A, I53V, I70L, M96L, V107D AND C113A.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 19

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.86 % / Description: NONE
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREE CELSIUS WITH THE 7.8 MONOACYLGLYCEROL (7.8 MAG) AS THE HOSTING LIPID.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03320, 0.97944
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 13, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.979441
ReflectionResolution: 2.05→58.04 Å / Num. obs: 62716 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.05→51.894 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 20.52 / Stereochemistry target values: ML
Details: THE 6 CHAINS FORMING 2 TRIMERS PER ASYMMETRIC UNIT COULD BE RELATED BY NCS HOWEVER THIS WAS DETRIMENTAL TO REFINEMENT AND SO WAS NOT USED. FOR THE MAJORITY OF THE REFINEMENT THE PHASES FROM ...Details: THE 6 CHAINS FORMING 2 TRIMERS PER ASYMMETRIC UNIT COULD BE RELATED BY NCS HOWEVER THIS WAS DETRIMENTAL TO REFINEMENT AND SO WAS NOT USED. FOR THE MAJORITY OF THE REFINEMENT THE PHASES FROM SEMET DATA WERE USED, TARGET MLHL, UNTIL THE FINAL ROUNDS OF REFINEMENT WHERE TARGET WAS ML. THE FOLLOWING RESIDUES COULD NOT BE PLACED INTO ELECTRON DENSITY DUE TO DISORDER OR FLEXIBILITY - A1-5, B1-23, C1-31, D1-13, E1-35, E47-49, F1-33.
RfactorNum. reflection% reflection
Rfree0.2167 3161 5.1 %
Rwork0.1959 --
obs0.1969 62622 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.383 Å2
Refinement stepCycle: LAST / Resolution: 2.05→51.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4416 0 306 187 4909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034932
X-RAY DIFFRACTIONf_angle_d0.5366687
X-RAY DIFFRACTIONf_dihedral_angle_d14.951866
X-RAY DIFFRACTIONf_chiral_restr0.039836
X-RAY DIFFRACTIONf_plane_restr0.002797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08060.32861380.28352567X-RAY DIFFRACTION99
2.0806-2.11310.26921390.26692519X-RAY DIFFRACTION99
2.1131-2.14780.27471700.24992525X-RAY DIFFRACTION100
2.1478-2.18480.27841320.22582549X-RAY DIFFRACTION100
2.1848-2.22450.26511200.24242557X-RAY DIFFRACTION100
2.2245-2.26730.36451310.33052502X-RAY DIFFRACTION98
2.2673-2.31360.26871450.22772548X-RAY DIFFRACTION99
2.3136-2.36390.2221540.18552551X-RAY DIFFRACTION100
2.3639-2.41890.19141360.16592583X-RAY DIFFRACTION100
2.4189-2.47940.21361160.16392566X-RAY DIFFRACTION100
2.4794-2.54640.20491100.16912602X-RAY DIFFRACTION100
2.5464-2.62130.17561410.16532564X-RAY DIFFRACTION100
2.6213-2.70590.19191470.16212583X-RAY DIFFRACTION100
2.7059-2.80270.20151290.16582560X-RAY DIFFRACTION100
2.8027-2.91490.19531220.17342595X-RAY DIFFRACTION100
2.9149-3.04750.2251320.17172613X-RAY DIFFRACTION100
3.0475-3.20820.19931510.17362573X-RAY DIFFRACTION100
3.2082-3.40910.20781420.18132606X-RAY DIFFRACTION100
3.4091-3.67230.18741440.18052601X-RAY DIFFRACTION100
3.6723-4.04170.1981450.1782622X-RAY DIFFRACTION100
4.0417-4.62620.17651410.17152645X-RAY DIFFRACTION100
4.6262-5.82730.24081300.22392675X-RAY DIFFRACTION100
5.8273-51.91050.2461460.23322755X-RAY DIFFRACTION99
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)
12.8943-1.60451.58211.3769-0.7387.5994-0.0831-0.019-0.50130.14290.00310.0820.55920.01640.10080.2263-0.09910.02670.2730.010.351735.731661.133187.7602
23.18710.06580.15464.29912.33195.7789-0.02040.06660.1041-0.1568-0.16160.1773-0.6629-0.12630.18620.11970.0122-0.0050.20180.02350.207443.000872.353981.8209
31.6603-0.6219-2.13732.47822.80983.5495-0.1542-0.1507-0.22650.46050.2339-0.12610.74910.5148-0.03610.23240.0639-0.02190.3281-0.00840.301655.919857.855982.749
42.55880.00390.58442.7940.39312.70230.01130.1955-0.20640.20780.10190.05360.7328-0.4637-0.00410.1626-0.04220.0040.18480.02440.264444.466258.116485.2764
51.08081.277-0.37576.68283.33185.54790.3714-0.13321.134-0.6634-0.65030.0715-0.3924-0.09640.27140.34070.06420.12720.41560.01580.581955.417277.779667.5259
62.2427-0.7066-2.34141.95810.29923.20340.091-0.33010.10530.29340.117-0.1954-0.27430.5533-0.19310.15-0.0459-0.02020.3054-0.02240.254358.12970.37383.8236
71.6336-0.25-1.21373.8337-0.39522.974-0.0603-0.03840.02620.13890.0629-0.12310.1390.1599-0.01180.16680.0201-0.01550.211-0.03440.234271.634750.033862.807
83.4837-0.5308-1.30714.12652.43778.8106-0.12110.2639-0.18670.0758-0.2510.41640.35-0.7890.30160.2240.00580.02080.2208-0.02560.373162.179342.317160.2712
93.28650.8288-1.56193.21811.9682.06140.0351-0.0177-0.34060.15260.1648-0.32270.24611.0095-0.12750.23680.1395-0.00610.3383-0.07370.377180.498439.11459.5171
104.432-0.5471-0.80996.8295-6.01895.68320.4021-0.34580.22731.10710.3199-0.8379-0.39432.8110.41881.1816-0.0563-0.07452.1323-0.04440.188886.479844.289283.9134
119.0523.6042-2.68147.8913-1.74067.28950.15870.2987-0.88650.34920.1401-0.13810.5938-0.1999-0.29191.2071-0.25270.0260.6322-0.07671.667657.918626.444761.9196
121.8825-0.34920.22572.40741.39883.5693-0.1053-0.2459-0.26940.60370.01580.19462.0097-0.3692-0.0440.6687-0.02880.0270.20980.00340.313968.932230.423161.8974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:47)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 48:121)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 24:83)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 84:121)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 32:57)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 58:121)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 14:80)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 81:121)
9X-RAY DIFFRACTION9(CHAIN E AND RESID 36:116)
10X-RAY DIFFRACTION10(CHAIN E AND RESID 117:121)
11X-RAY DIFFRACTION11(CHAIN F AND RESID 29:37)
12X-RAY DIFFRACTION12(CHAIN F AND RESID 38:121)

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