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- PDB-4d2e: Crystal structure of an integral membrane kinase - v2.3 -

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Basic information

Entry
Database: PDB / ID: 4d2e
TitleCrystal structure of an integral membrane kinase - v2.3
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / DGKA / IN MESO CRYSTALLIZATION / IN VITRO EXPRESSION / LIPID METABOLISM / LIPIDIC MESOPHASE / LIPIDIC CUBIC PHASE / LCP / MEMBRANE PROTEIN / MICROCRYSTAL / 7.8 MAG / THERMOSTABLE MUTANT
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / phosphorylation / 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 / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLi, D. / Boland, C. / Caffrey, M.
CitationJournal: Cell.Mol.Life Sci. / Year: 2014
Title: Cell-Free Expression and in Meso Crystallisation of an Integral Membrane Kinase for Structure Determination.
Authors: Boland, C. / Li, D. / Shah, S.T.A. / Haberstock, S. / Dotsch, V. / Bernhard, F. / Caffrey, M.
History
DepositionMay 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Feb 27, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Oct 9, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,35428
Polymers85,2276
Non-polymers6,12722
Water2,594144
1
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,01617
Polymers42,6133
Non-polymers4,40214
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-82 kcal/mol
Surface area16200 Å2
MethodPISA
2
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,33811
Polymers42,6133
Non-polymers1,7248
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-129 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.290, 91.820, 143.920
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: CELL-FREE EXPRESSION / Plasmid: PET22B-DGKA-DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): A19 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Non-polymers , 6 types, 166 molecules

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


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


Mass: 314.460 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H34O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN ...THE PROTEIN CONTAINS AN N-TERMINAL 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: 2

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.97 %
Description: THE PRESENCE OF ZINC IN THE STRUCTURE WAS CONFIRMED BY A X-RAY FLUORESCENCE SCAN AND WAS SUPPORTED BY A DATA SET COLLECTED AT THE ZINC EDGE (1.282400 A) WHICH IS AVAILABLE IN THIS ENTRY.
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 3-5%(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD WITH 7. ...Details: 3-5%(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD WITH 7.8 MAG AS THE HOST LIPID AT 4 CELSIUS DEGREE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2014 / 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 wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.28→75.29 Å / Num. obs: 45427 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 39.04 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.9 / % possible all: 96.9

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Processing

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

3ze3


Resolution: 2.28→52.021 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2263 5 %
Rwork0.1884 --
obs0.1904 45339 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.66 Å2
Refinement stepCycle: LAST / Resolution: 2.28→52.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 424 144 5109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125318
X-RAY DIFFRACTIONf_angle_d0.9957138
X-RAY DIFFRACTIONf_dihedral_angle_d22.6372026
X-RAY DIFFRACTIONf_chiral_restr0.038862
X-RAY DIFFRACTIONf_plane_restr0.004853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2801-2.32970.29281470.25362581X-RAY DIFFRACTION96
2.3297-2.38390.28691510.23192582X-RAY DIFFRACTION97
2.3839-2.44350.24971270.20642618X-RAY DIFFRACTION96
2.4435-2.50960.24841260.19592644X-RAY DIFFRACTION97
2.5096-2.58340.24811190.19042644X-RAY DIFFRACTION97
2.5834-2.66680.22871540.17362593X-RAY DIFFRACTION96
2.6668-2.76210.25421250.16882610X-RAY DIFFRACTION96
2.7621-2.87270.20221320.15942678X-RAY DIFFRACTION98
2.8727-3.00340.20191440.16372732X-RAY DIFFRACTION100
3.0034-3.16180.21151550.15642729X-RAY DIFFRACTION100
3.1618-3.35980.20481500.17782714X-RAY DIFFRACTION100
3.3598-3.61920.18651490.18562761X-RAY DIFFRACTION100
3.6192-3.98330.26631440.20952712X-RAY DIFFRACTION98
3.9833-4.55940.18631520.15382762X-RAY DIFFRACTION100
4.5594-5.74320.24621390.20482818X-RAY DIFFRACTION100
5.7432-52.03430.25141490.21462898X-RAY DIFFRACTION98
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)
10.0808-0.04750.11950.21220.01550.2819-0.37430.1138-0.06070.08620.3386-0.17580.41240.21860.00040.4560.02870.03070.336-0.04740.3015-2.065710.6551-22.1808
20.51490.4933-0.03610.64230.16230.0890.02020.0343-0.177-0.126-0.16-0.1444-0.14840.0054-00.1870.0163-0.01510.27480.02340.2758-1.245921.3847-9.1951
30.62590.47090.1210.8877-0.16610.7056-0.1093-0.1010.13450.3790.11210.049-0.8724-0.215-0.00450.31040.0239-0.01160.237-0.02110.2776-6.805131.7543-10.5929
40.28140.0755-0.10.2549-0.12310.1415-0.18930.3177-0.2937-0.39080.2457-0.01790.41330.1188-0.00060.4101-0.15380.01540.43460.01220.4188-21.81597.5794-8.8583
50.4831-0.2280.19210.42240.04260.1398-0.04520.0086-0.1289-0.14690.0556-0.00810.2901-0.1603-00.196-0.00510.01050.22610.01270.2513-11.041214.4905-13.6553
60.401-0.13390.01190.2471-0.12340.7330.4833-0.01550.8142-0.0338-0.4208-0.20640.42060.574-0.01690.5620.00240.17580.2846-0.00290.6559-20.023834.79471.845
70.18560.2852-0.06990.3988-0.06930.02680.0391-0.0397-0.0497-0.07590.02580.0148-0.3087-0.2878-00.2130.04080.01980.30130.02650.2487-15.895427.9123-10.0478
80.73050.1043-0.18070.21640.02520.18150.15960.21150.0463-0.00760.12570.19970.0657-0.3376-0.01210.1079-0.0085-0.02040.3040.04130.2246-23.317921.797-10.3593
90.0873-0.0688-0.08710.06460.0540.06630.09550.05810.35890.3899-0.13590.16440.10180.05110.00010.30260.01790.03010.28850.02180.2747-39.22728.719618.7809
100.12290.1567-0.13020.2514-0.15930.1245-0.29570.10530.2243-0.40960.11510.08570.43150.16530.00010.4474-0.0618-0.00090.36010.02840.3226-31.27587.50830.645
110.2640.073-0.13360.3704-0.16220.10190.01860.0407-0.1086-0.07880.1376-0.0311-0.60060.77310.00090.3128-0.0337-0.0040.2179-0.0030.266-33.0948-0.751112.0162
120.02980.0152-0.02020.02150.01510.0714-0.0905-0.00110.0399-0.00240.08560.02170.0344-0.03860.00060.8784-0.2206-0.07280.96730.33660.6173-22.7829-1.844434.3594
130.56320.1623-0.19890.78640.05480.0777-0.1492-0.0455-0.1426-0.18920.0758-0.28450.46590.1140.00020.34330.00740.03750.24240.04060.2958-24.7037-4.03135.5623
140.0299-0.0768-0.00330.29950.00180.00020.12980.0272-0.509-0.13430.0433-0.07250.0555-0.09630.01260.6932-0.41730.05260.98270.091.022-49.8135-16.13465.1728
151.4425-0.25480.24181.0065-0.30520.1249-0.2447-0.5163-0.13130.2070.49710.48070.1916-0.56980.04920.3068-0.2422-0.04730.21190.06250.3072-41.1929-7.998518.3004
160.47980.0905-0.06390.539-0.20610.07370.03930.02310.1220.0275-0.04690.06360.0373-0.4392-0.00060.291-0.02090.00230.36260.03660.2603-44.0609-0.73344.8361
170.0979-0.00420.00070.10020.01060.063-0.37390.2496-0.2085-0.0253-0.3841-0.18090.01350.2669-0.0130.86440.2820.14470.64110.10650.5551-21.7864-18.24322.514
180.59810.39640.12050.4706-0.04570.11330.0269-0.0908-0.1228-0.09470.0324-0.1290.62550.2512-00.42350.02390.00530.24720.02510.2939-30.9762-11.7817.451
191.18440.0664-0.15060.38610.38331.4040.0635-0.2414-0.3325-0.36130.02490.13450.5966-0.160.25651.0455-0.2332-0.0448-0.1121-0.18260.2663-36.1537-19.34534.4137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 28 THROUGH 82 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 83 THROUGH 121 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 23 THROUGH 51 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 52 THROUGH 121 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 29 THROUGH 51 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 52 THROUGH 82 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 83 THROUGH 121 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 14 THROUGH 28 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 29 THROUGH 51 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 52 THROUGH 82 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 83 THROUGH 87 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 88 THROUGH 121 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 19 THROUGH 51 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 52 THROUGH 90 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 91 THROUGH 121 )
17X-RAY DIFFRACTION17CHAIN 'F' AND (RESID 29 THROUGH 51 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 52 THROUGH 92 )
19X-RAY DIFFRACTION19CHAIN 'F' AND (RESID 93 THROUGH 120 )

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