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

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Basic information

Entry
Database: PDB / ID: 4brr
TitleCrystal structure of the integral membrane diacylglycerol kinase - delta 7.79
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / DGKA / IN MESO CRYSTALLIZATION / LOW TEMPERATURE CRYSTALLIZATION / MEMBRANE PROTEIN / LCP / LIPIDIC CUBIC PHASE / LIPID MESOPHASE
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
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / ACETATE ION / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsLi, D. / Howe, N. / Caffrey, M.
CitationJournal: To be Published
Title: Crystal Structure of an Integral Membrane Enzyme Determined by X-Ray Free Electron Laser Femtocrystallography
Authors: Li, D. / Howe, N. / Caffrey, M.
History
DepositionJun 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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)86,52612
Polymers85,2276
Non-polymers1,2996
Water1086
1
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2705
Polymers42,6133
Non-polymers6572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-69.1 kcal/mol
Surface area19570 Å2
MethodPISA
2
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2557
Polymers42,6133
Non-polymers6424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-56 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.060, 91.500, 143.720
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) / Plasmid: PTRCHISB-DGKA-DELTA 7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-79M / (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / [(2R)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H36O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 3.9 Å3/Da / Density % sol: 68.47 % / Description: NONE
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 60 MM MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 4-6 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 60 MM MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 7.9 MONOACYLGLYCEROL (7.9 MAG) AS THE HOSTING LIPID.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03315
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.44→75.06 Å / Num. obs: 37160 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 51.52 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.6
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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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 3ZE3

3ze3


Resolution: 2.44→66.533 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 28.12 / Stereochemistry target values: ML
Details: THERE ARE THREE NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT THE NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2522 1847 5 %
Rwork0.2178 --
obs0.2195 37090 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.27 Å2
Refinement stepCycle: LAST / Resolution: 2.44→66.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 87 6 4563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074627
X-RAY DIFFRACTIONf_angle_d0.6886307
X-RAY DIFFRACTIONf_dihedral_angle_d11.4281603
X-RAY DIFFRACTIONf_chiral_restr0.045798
X-RAY DIFFRACTIONf_plane_restr0.002751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.5060.35861330.32572692X-RAY DIFFRACTION99
2.506-2.57970.34661210.28382704X-RAY DIFFRACTION99
2.5797-2.6630.28131570.2562671X-RAY DIFFRACTION99
2.663-2.75820.29661310.24422672X-RAY DIFFRACTION99
2.7582-2.86860.26141310.2282707X-RAY DIFFRACTION99
2.8686-2.99920.25961470.21632670X-RAY DIFFRACTION98
2.9992-3.15730.23531500.20762687X-RAY DIFFRACTION99
3.1573-3.35510.23581490.21422698X-RAY DIFFRACTION99
3.3551-3.61410.25321470.2062711X-RAY DIFFRACTION99
3.6141-3.97780.23031460.19712711X-RAY DIFFRACTION98
3.9778-4.55330.2221520.17412728X-RAY DIFFRACTION99
4.5533-5.73610.27881370.22422754X-RAY DIFFRACTION98
5.7361-66.55740.24231460.23212838X-RAY DIFFRACTION97
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)
17.9694-5.6009-2.41014.90350.88124.9972-0.9183-0.79120.68140.89110.7454-0.3926-0.9082-0.48230.18170.6210.027-0.04350.7282-0.16610.3962-1.2586-11.539722.5959
24.7179-0.6920.34141.75921.74541.9708-0.1985-0.05840.05450.12680.026-0.19860.2974-0.23360.18730.2860.00630.01360.35610.00840.306-1.0176-21.35439.4533
37.92211.347-1.83146.9886-0.22350.43940.216-0.1245-0.0809-0.0318-0.1082-0.08350.2235-0.23470.14240.330.0587-0.03820.2504-0.10460.3812-6.2389-31.31029.7274
48.6312-1.79010.97899.05621.21117.3647-0.3585-1.16250.25711.09160.45460.6849-1.1619-0.64-0.16030.42770.13450.00480.54470.02530.6381-21.7865-7.46498.8024
53.85341.0415-0.05573.107-1.51885.90440.0019-0.13030.16590.44120.160.0568-0.8305-0.049-0.15850.34410.05660.01380.2212-0.02860.315-10.8741-14.406213.8918
67.61023.9816-2.74963.6614-4.04626.62090.42340.7768-1.2747-0.7271-0.7924-0.339-0.04930.08230.62460.83110.0785-0.19350.4939-0.18990.7983-19.5387-33.5442-4.427
73.5363-0.67931.4162.5949-0.29758.47350.1404-0.4389-0.09790.33120.07960.32080.3064-0.6576-0.17150.321-0.07490.00990.40340.05250.3159-20.0418-24.407110.5227
82.95960.83441.43485.3467-0.41163.721-0.08460.0846-0.13210.10090.0752-0.0306-0.14180.03530.02270.33820.06760.02330.40020.0390.3302-33.9663-3.9623-9.657
95.54810.3168-1.2225.2216-4.09168.6125-0.2560.1179-0.01630.0804-0.3489-0.4164-0.38020.93160.61320.31960.0048-0.09140.37710.00230.4905-24.20083.8292-9.9552
101.49760.58430.66280.91550.48040.5339-0.6892-0.94351.24810.42510.09450.60990.0802-0.34140.5150.56240.65890.30051.69390.37961.7086-50.384513.9220.8099
113.44981.33221.06092.9263-0.63171.79430.10620.11860.21170.01980.04830.1002-0.5201-1.2106-0.15480.3920.14930.01330.47840.06370.3774-42.37595.0068-12.5078
122.53443.0404-3.04563.6499-3.65543.6635-0.5137-0.9797-0.16890.379-0.5882-1.4067-1.44280.32890.90381.3318-0.134-0.13481.06640.01241.1224-22.559918.52450.9444
132.1316-0.8374-0.22042.9141-2.47997.92450.20530.0706-0.1483-0.02950.0893-0.0534-1.14320.6098-0.37310.421-0.03810.01960.369-0.02040.4442-30.514511.6421-17.5436
146.99031.33120.99195.00123.34053.7187-0.2001-0.69510.57780.2155-0.0262-0.0461-2.3101-1.02360.32830.85630.2025-0.06970.37550.01170.4824-36.66119.2626-5.9159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 8 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 120 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 33 THROUGH 51 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 52 THROUGH 121 )
8X-RAY DIFFRACTION8CHAIN D AND (RESID 14 THROUGH 82 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 83 THROUGH 121 )
10X-RAY DIFFRACTION10CHAIN E AND (RESID 34 THROUGH 51 )
11X-RAY DIFFRACTION11CHAIN E AND (RESID 52 THROUGH 120 )
12X-RAY DIFFRACTION12CHAIN F AND (RESID 33 THROUGH 51 )
13X-RAY DIFFRACTION13CHAIN F AND (RESID 52 THROUGH 90 )
14X-RAY DIFFRACTION14CHAIN F AND (RESID 91 THROUGH 120 )

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