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- PDB-4cjz: Crystal structure of the integral membrane diacylglycerol kinase ... -

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Basic information

Entry
Database: PDB / ID: 4cjz
TitleCrystal structure of the integral membrane diacylglycerol kinase DgkA- 9.9, delta 4
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / IN MESO CRYSTALLISATION / LCP / LIPID CUBIC PHASE / LIPIDIC MESOPHASE / LIPID METABOLISM / MEMBRANE PROTEIN / MICROCRYSTAL / MONOACYLGLYCEROL / MONOOLEIN / 9.9 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 / membrane / identical protein binding / 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 (9Z)-octadec-9-enoate / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsLi, D. / Aragao, D. / Pye, V.E. / Caffrey, M.
CitationJournal: To be Published
Title: Crystal Structure of the Integral Membrane Diacylglycerol Kinase with Zn-Amppcp Bound and its Catalytic Mechanism
Authors: Li, D. / Caffrey, M.
History
DepositionDec 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Mar 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 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Mar 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 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

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Assembly

Deposited unit
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0784
Polymers42,7223
Non-polymers3571
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-89.7 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.780, 72.780, 199.280
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 / DIACYLGLYCEROL KINASE -DELTA 4


Mass: 14240.527 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTRCHISB-DGKA-DELTA 4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
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 FOUR 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: 4.14 Å3/Da / Density % sol: 70.32 % / Description: NONE
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 7-8 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 2-4 %(V/V) 1,4-BUTANEDIOL, 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 ...Details: 7-8 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 2-4 %(V/V) 1,4-BUTANEDIOL, 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 DEGREES CELCIUS WITH THE 9.9 MONOACYLGLYCEROL (9.9 MAG, MONOOLEIN) AS THE HOSTING LIPID.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 21, 2011 / 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: 3.25→53.27 Å / Num. obs: 10196 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 108.82 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.7
Reflection shellResolution: 3.25→3.33 Å / Redundancy: 10 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZE5

3ze5


Resolution: 3.25→53.267 Å / SU ML: 0.39 / σ(F): 1.37 / Phase error: 34.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2915 475 4.7 %
Rwork0.2554 --
obs0.2573 10166 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 142.58 Å2
Refinement stepCycle: LAST / Resolution: 3.25→53.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 25 0 2596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022641
X-RAY DIFFRACTIONf_angle_d0.4053593
X-RAY DIFFRACTIONf_dihedral_angle_d9.905907
X-RAY DIFFRACTIONf_chiral_restr0.028444
X-RAY DIFFRACTIONf_plane_restr0.001428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.72020.33841480.27583171X-RAY DIFFRACTION100
3.7202-4.68670.27841550.24823203X-RAY DIFFRACTION100
4.6867-53.27390.28891720.25453317X-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)
16.0112-0.9389-1.29524.27283.98384.25670.63740.10050.63240.04740.2501-0.58520.0682-0.0187-0.80481.354-0.1012-0.16920.97880.05630.8782-20.87163.5831-8.4121
23.96432.18370.69715.21411.51242.1671-0.20750.0912-0.05860.1188-0.468-0.5275-2.04431.4130.47541.2703-0.2027-0.10020.80550.03660.9206-27.327211.0499-14.2127
31.1661-0.09483.30510.0065-0.25089.5165-0.27880.7569-0.7830.1968-0.5628-2.0906-0.59910.86720.33031.7513-0.02730.07611.7057-0.42971.5897-27.601921.2379-34.4087
43.69281.592.39174.9671.15382.0140.23550.12240.0844-0.44570.11760.2654-0.6597-0.08-0.68741.5246-0.1856-0.08680.5310.04130.9824-28.502519.5333-3.4653
55.6320.28471.1574.1831-0.96985.1530.2038-0.0526-0.1619-0.4254-0.13830.65010.1188-1.7682-0.14811.4805-0.3662-0.04961.2962-0.0611.0012-47.18543.2595-11.4554
63.4262-0.750.18815.9891-0.28285.37620.02230.0272-0.045-0.3076-0.2906-0.26670.8214-0.30580.21841.0901-0.2956-0.08310.5022-0.01380.7592-33.18792.7483-11.5753
74.9126-1.95790.99332.99460.84439.93990.12310.55520.40380.319-0.02390.4168-2.6265-0.4529-0.00211.8583-0.0839-0.10131.0379-0.17551.4138-39.311525.5765-7.3434
83.4869-0.9203-1.16032.27322.89173.30220.15140.12840.1308-0.3749-0.60640.2636-1.4057-1.36930.36141.2691-0.2281-0.01911.0103-0.03030.9471-41.709213.4619-12.3155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 7 THROUGH 51 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 52 THROUGH 86 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 87 THROUGH 91 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 92 THROUGH 120 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 5 THROUGH 51 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 52 THROUGH 121 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 16 THROUGH 51 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 52 THROUGH 119 )

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