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- PDB-3ze5: Crystal structure of the integral membrane diacylglycerol kinase ... -

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Basic information

Entry
Database: PDB / ID: 3ze5
TitleCrystal structure of the integral membrane diacylglycerol kinase - delta4
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / CLLD / 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 / 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
Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsLi, D. / Vogeley, L. / Pye, V.E. / Lyons, J.A. / 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)42,7223
Polymers42,7223
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-93.7 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.740, 72.740, 198.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 14240.527 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria)
Description: THE 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_DELTA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)
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 I53C, I70L, M96L AND V107D.

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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: 3.56 Å3/Da / Density % sol: 65.49 % / 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: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.1→60.05 Å / Num. obs: 11008 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 107.84 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 90.9

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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: 3.101→45.678 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 32.81 / Stereochemistry target values: ML
Details: THE 3-FOLD SYMMETRY BETWEEN CHAINS A, B AND C WAS NOT HELPFUL FOR REFINEMENT AND THEREFORE NOT USED.
RfactorNum. reflection% reflection
Rfree0.2581 526 4.8 %
Rwork0.232 --
obs0.2335 10990 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.88 Å2
Refinement stepCycle: LAST / Resolution: 3.101→45.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 0 0 2569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032615
X-RAY DIFFRACTIONf_angle_d0.543565
X-RAY DIFFRACTIONf_dihedral_angle_d12.199886
X-RAY DIFFRACTIONf_chiral_restr0.036441
X-RAY DIFFRACTIONf_plane_restr0.002427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1006-3.41250.38361340.29962474X-RAY DIFFRACTION91
3.4125-3.90610.28781110.24082571X-RAY DIFFRACTION94
3.9061-4.92030.2311320.19612669X-RAY DIFFRACTION96
4.9203-45.68250.24911490.24152750X-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)
16.7375-0.19971.71086.4283-0.84987.50540.60020.83410.0184-0.7234-0.26481.07510.5833-1.2393-0.02740.98230.20430.15090.7065-0.03030.5143-61.047917.192717.7453
26.28752.2101-0.45831.8088-0.52211.7929-0.2139-1.137-0.91560.438-0.1173-0.1626-0.0751-0.15180.15941.08680.5450.06880.55850.24820.2587-52.738416.308637.6905
36.73592.6712-2.05283.9521-0.32640.7138-0.78021.0356-1.1753-1.6105-0.00540.33210.94060.1463-0.07291.27570.37770.15080.6933-0.04280.465-49.467616.64689.5906
42.9587-0.95-0.64232.4012-0.53243.3572-0.30010.1673-0.2405-0.1250.0903-0.00830.44140.7159-0.68190.97340.68280.14010.88580.17090.7439-41.580114.315224.4715
55.6942-0.04251.00754.46921.82692.52380.0507-0.2683-0.133-0.99830.435-0.1345-1.53491.0848-0.3651.07280.04780.26031.55950.30810.6106-40.642339.156913.6237
62.092-1.48951.00352.4586-1.35212.14520.34930.54520.2185-0.8073-0.0680.224-0.5254-0.250.14941.41690.8730.02560.48890.02260.7076-52.96838.120731.7167
72.8531-0.7375-1.23491.04990.44073.8548-0.5050.7344-0.53970.1819-0.27740.69010.0666-0.2075-0.63370.95060.52790.02880.76930.19220.3771-52.700826.445115.1968
84.37423.36790.26615.57450.93525.5847-0.0586-1.4131.26561.5845-0.45330.8268-0.4077-0.6089-0.53431.05260.63670.35150.6251-0.584-0.0369-57.763828.510839.1829
94.28663.6844.40555.59356.55257.66721.47460.54230.50550.74550.4337-0.19270.52411.4514-0.59841.4883-0.0616-0.15981.47370.57511.1817-31.630614.180515.5044
103.77310.7225-1.87574.07992.58883.3573-0.78390.4504-0.583-0.11730.6147-0.2039-0.35851.9551-0.21551.20140.3472-0.04751.80050.14210.983-31.015123.903231.253
113.42150.19351.08243.6715-0.01941.00560.10980.0799-0.60920.06330.01670.57910.39122.1987-0.13090.92010.3522-0.03631.18380.07320.5333-38.704124.140529.8521
125.6099-0.03950.42144.60341.49797.0582-0.56780.6078-0.1093-0.0347-0.011-0.7054-0.30392.5359-0.35740.69760.18380.05430.6130.09810.577-40.654530.667116.9583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:36)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 37:65)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 66:85)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 86:121)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 5:29)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 30:53)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 54:106)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 107:120)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 15:26)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 27:53)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 54:69)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 70:120)

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