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- PDB-3ze4: Crystal structure of the integral membrane diacylglycerol kinase ... -

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Basic information

Entry
Database: PDB / ID: 3ze4
TitleCrystal structure of the integral membrane diacylglycerol kinase - wild-type
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / LIPID METABOLISM / IN MESO CRYSTALLISATION / LIPID CUBIC PHASE / LIPIDIC MESOPHASE / MEMBRANE PROTEIN / 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
Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.702 Å
Model type detailsP ATOMS ONLY, CHAIN D, E, F
AuthorsLi, D. / Lyons, J.A. / Pye, V.E. / 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 / Other / Structure summary / Category: audit_author / database_2 / pdbx_database_status
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
Revision 1.6Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)42,7583
Polymers42,7583
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-82.7 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.970, 74.970, 196.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESSEQ 11 OR CHAIN A AND RESSEQ...
211CHAIN B AND RESSEQ 11 OR CHAIN B AND RESSEQ...
311CHAIN C AND RESSEQ 11 OR CHAIN C AND RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(-0.5142, 0.8576, 0.009619), (-0.8471, -0.5096, 0.1511), (0.1345, 0.06954, 0.9885)-93.03, -8.116, 5.143
2given(-0.4896, -0.8618, 0.1326), (0.8719, -0.4853, 0.06559), (0.007839, 0.1477, 0.989)-53.5, 75.43, -2.996

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Components

#1: Protein DIACYLGLYCEROL KINASE / DAGK / DIGLYCERIDE KINASE / DGK


Mass: 14252.625 Da / Num. of mol.: 3
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.
Plasmid: PTRCHISB_DGKA_WILD-TYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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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: 3.74 Å3/Da / Density % sol: 67.16 % / 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, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREE ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 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: 1.03306
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 13, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03306 Å / Relative weight: 1
ReflectionResolution: 3.7→39.23 Å / Num. obs: 7069 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 130.23 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 98

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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 3ZE5

3ze5


Resolution: 3.702→39.226 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 37.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3118 333 4.7 %
Rwork0.2848 --
obs0.2862 7069 96.73 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 150.08 Å2
Refinement stepCycle: LAST / Resolution: 3.702→39.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 0 0 2458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052499
X-RAY DIFFRACTIONf_angle_d0.7953405
X-RAY DIFFRACTIONf_dihedral_angle_d13.044850
X-RAY DIFFRACTIONf_chiral_restr0.052431
X-RAY DIFFRACTIONf_plane_restr0.002403
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A451X-RAY DIFFRACTIONPOSITIONAL
12B451X-RAY DIFFRACTIONPOSITIONAL0.022
13C343X-RAY DIFFRACTIONPOSITIONAL0.019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7016-4.66240.3251570.30283363X-RAY DIFFRACTION98
4.6624-39.22780.30631760.27633373X-RAY DIFFRACTION95
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)
12.9161.5871.43130.8620.76640.6879-0.9293-0.64512.4374-0.469-0.52540.2201-1.1222-0.7439-0.31261.42750.52530.01741.48290.38191.4305-69.100428.184115.9771
20.0359-0.06010.03310.1061-0.06080.03120.07860.2373-0.8514-1.06081.22211.05231.1092-0.92540.01261.84790.3162-0.10061.53120.08461.0787-63.198412.777115.0365
30.34550.4269-0.25240.5269-0.31340.1831-1.35170.1189-0.7963-1.39891.5755-0.41740.6970.6337-0.0061.98780.27690.16921.67650.37331.701-55.02827.1520.2831
42.9751.0642-1.84910.4582-0.82981.8956-0.4091-1.6446-0.99140.84650.62530.7133-1.2961-0.1778-0.15821.23480.48220.24961.06130.18121.6679-54.312314.281239.3475
50.07960.15330.00461.6242-3.49859.92060.1383-0.17910.1852-0.71370.6136-0.58821.6594-0.84470.29630.90310.48870.24961.1110.1650.8159-51.168816.999321.4484
61.36180.9691-1.36290.7043-0.95591.3759-1.41760.7891-2.3586-1.57870.9573-0.67512.20571.444-0.06941.6760.15770.04792.1565-0.35541.1111-49.363614.459-1.7017
77.32231.87291.51990.47960.39180.31440.10042.20740.6042-0.56391.1807-1.1984-1.01340.20640.15442.99750.50290.50961.6473-0.24491.4082-40.673815.36357.2886
80.98060.0035-0.00790.1078-0.25020.6172-0.07650.9188-0.6717-0.529-0.26270.13730.24210.2054-1.51710.89781.32630.02040.5646-0.3171.1679-42.945414.027827.408
90.11060.09280.13231.004-1.02491.7825-0.4401-0.1692-0.2539-0.1766-0.34560.37920.20050.2932-2.16561.75391.2023-0.05710.04610.76330.773-42.916612.83943.3136
100.2410.3047-0.24911.70730.63270.9535-0.1789-0.1396-0.5357-0.9324-0.0006-0.5447-1.48670.62510.05711.44440.2750.07311.79150.51111.172-43.598539.443312.8263
111.0967-0.23340.12741.5927-0.15612.92280.5172-0.007-0.37470.25690.72670.21440.34980.24810.2262.15840.8686-0.15830.55390.11610.8308-55.56138.479930.7327
122.02420.2888-0.6660.3019-0.46180.6453-0.4002-0.014-0.07180.53550.23510.394-0.222-0.7418-0.00121.20960.4519-0.04410.93080.02120.5875-52.691427.95615.4786
132.37320.9262.63853.44912.63368.3477-0.1856-0.15350.26551.4404-1.12350.54911.1829-1.0276-0.43381.33420.4720.21310.61320.12340.972-58.838225.079128.7914
140.56140.5521-0.09150.5918-0.0470.05690.6140.9956-0.980.06670.92180.48110.62971.04620.00261.20470.2716-0.09132.35380.10341.7-30.646124.535929.1579
153.34890.262-0.81373.1697-1.52851.6821-1.08520.35970.22740.5158-0.1178-0.8416-1.0832.3514-0.03490.95440.3429-0.0151.3640.01730.9091-41.667828.911420.0409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:17)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 18:27)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 28:37)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 38:57)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 58:77)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 78:87)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 88:97)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 98:112)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 113:120)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 8:29)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 30:51)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 52:91)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 92:120)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 28:51)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 52:119)

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