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- PDB-4brb: Crystal structure of the integral membrane enzyme DgkA-ref, delta 7 -

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Basic information

Entry
Database: PDB / ID: 4brb
TitleCrystal structure of the integral membrane enzyme DgkA-ref, delta 7
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / LIPID METABOLISM / MEMBRANE PROTEIN
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)-PENTADEC-7-ENOATE / ACETATE ION / CITRATE ANION / Diacylglycerol kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLi, D. / Caffrey, M.
CitationJournal: Sci.Rep. / Year: 2014
Title: Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic.
Authors: Li, D. / Caffrey, M.
History
DepositionJun 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: 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)88,68519
Polymers85,2276
Non-polymers3,45813
Water37821
1
A: DIACYLGLYCEROL KINASE
B: DIACYLGLYCEROL KINASE
C: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,12911
Polymers42,6133
Non-polymers2,5168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-83.2 kcal/mol
Surface area15770 Å2
MethodPISA
2
D: DIACYLGLYCEROL KINASE
E: DIACYLGLYCEROL KINASE
F: DIACYLGLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5568
Polymers42,6133
Non-polymers9425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-113.3 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.500, 91.570, 143.570
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 / DIACYLGLYCEROL KINASE -DELTA 7


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTRCHISB-DGKA-DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Non-polymers , 5 types, 34 molecules

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


Mass: 314.460 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78N)
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 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: 1

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.43 % / Description: NONE
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 (LIPIDIC CUBIC PHASE) METHOD AT 4 ...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 (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS 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: SLS / Beamline: X10SA / Wavelength: 1.03319
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.55→71.79 Å / Num. obs: 32610 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 55.99 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.2 / % possible all: 97.9

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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: 2.55→45.233 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 27.42 / Stereochemistry target values: ML
Details: THERE ARE SIX NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2614 1634 5 %
Rwork0.2173 --
obs0.2196 32531 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.43 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 238 21 4762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014806
X-RAY DIFFRACTIONf_angle_d1.0556506
X-RAY DIFFRACTIONf_dihedral_angle_d14.2031732
X-RAY DIFFRACTIONf_chiral_restr0.064803
X-RAY DIFFRACTIONf_plane_restr0.003771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6250.31971380.2782528X-RAY DIFFRACTION98
2.625-2.70970.27461410.23452564X-RAY DIFFRACTION99
2.7097-2.80660.25441290.2272561X-RAY DIFFRACTION99
2.8066-2.91890.26941220.20692561X-RAY DIFFRACTION99
2.9189-3.05180.24331240.20292594X-RAY DIFFRACTION99
3.0518-3.21260.24551550.20342544X-RAY DIFFRACTION99
3.2126-3.41380.28471410.21542581X-RAY DIFFRACTION99
3.4138-3.67730.31941330.27482470X-RAY DIFFRACTION95
3.6773-4.04720.26631350.21962455X-RAY DIFFRACTION94
4.0472-4.63230.20271430.16772637X-RAY DIFFRACTION99
4.6323-5.83420.25821280.2222664X-RAY DIFFRACTION99
5.8342-45.24030.27381450.2262738X-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)
15.5344-1.7846-1.22832.61961.44055.654-0.2364-0.16740.53430.30570.1297-0.0169-0.3029-0.05080.04870.3668-0.07270.00280.36420.00150.421439.635330.376514.4951
26.49813.1981-4.92853.8073-4.6415.94430.06330.1708-0.0176-0.0881-0.4303-0.27850.18510.43420.44940.32720.04420.02150.22360.00820.292432.959424.89316.998
36.1812-0.86740.61727.25151.86653.55840.2374-0.9824-0.79761.33370.15740.50590.8706-0.245-0.54020.6189-0.13290.0730.45390.09970.413127.696112.453625.0446
45.32562.17821.42682.7330.23790.4469-0.87970.45150.3678-1.61560.0128-1.08591.25070.95560.82290.72130.20330.21160.53840.05810.474835.739818.0974-4.0318
53.9595-3.91752.53386.7311.22347.5684-0.4765-0.29630.11330.33910.07520.0802-0.4079-0.27070.13970.3042-0.016-0.04490.34730.01720.401618.086136.31515.7642
66.2142-1.24731.74326.9476-5.28064.0942-0.236-0.7470.36481.1850.1606-0.2483-1.6007-0.95470.0220.42470.05630.05070.3544-0.0110.431722.455327.58224.9112
74.27120.5598-0.67464.5433-5.86067.48650.0276-0.2420.17660.97810.0557-0.2851-1.3521.24460.04170.4141-0.0285-0.02440.2937-0.0560.357432.065129.047823.5369
83.6831.56640.10416.16396.88448.4806-0.12520.8896-0.2987-0.26930.2217-0.6935-1.62550.32540.07590.3743-0.1069-0.04560.35190.05320.381830.222138.9336-2.1218
97.94382.01021.25294.60835.26216.4534-0.0773-2.7832-0.35711.19090.4772-0.6781.38830.0427-0.0670.87620.0266-0.24720.99470.13460.900816.0578.63784.9479
106.52781.5098-0.11742.53410.28746.23280.26170.7334-0.617-0.6135-0.6465-0.1140.66020.40890.58340.53740.1308-0.05360.385-0.00770.423522.009617.3524-5.7542
112.98793.0966-4.02743.4141-4.50587.38780.4795-0.4941-0.33861.0925-0.05710.5173-0.1513-1.4369-0.92260.5528-0.0097-0.01180.4920.10470.417120.086916.724818.8531
123.87020.05511.74263.01390.78487.47050.1294-0.5752-0.10490.43070.31380.33610.1074-1.046-0.49420.19190.04160.01090.41380.03190.392214.866823.471511.4686
139.819-2.82441.56327.44884.05084.4102-0.36570.84350.0632-0.01320.21630.0052-0.30360.31340.12950.3305-0.05840.02070.28910.03960.18430.234737.3709-17.8188
149.1541-0.63891.20588.7596-1.11766.1454-0.3363-0.7205-0.24841.1628-0.2582-0.0118-0.67190.11650.6170.50330.01890.00060.29790.04610.35074.864442.22352.0464
157.47862.4046-3.86462.2754-1.49627.30130.10570.4832-0.093-0.13840.0042-0.81560.49971.33760.08750.57160.102-0.02210.55550.03630.53799.251248.091-25.5931
167.4308-0.6993-0.37427.2932-3.71791.9344-0.4791-0.6647-0.16970.8372-0.4958-0.5114-0.53340.73350.85770.4087-0.0317-0.0490.363-0.02910.356312.926548.9919-1.5611
171.996-8.27761.76276.8955-1.03381.4195-1.028-1.08210.42810.76210.719-0.3480.12760.0067-0.19351.19770.60250.86271.29170.9173.2337-13.355560.2474-2.9379
186.5491-0.8956-0.37547.01430.84070.1103-0.2972-0.95040.49941.2847-0.49480.5992-2.3671-3.20910.48241.05210.48010.06461.1601-0.06130.5394-6.29758.01483.4051
197.4492-0.44134.90657.56460.29153.3105-0.03011.0601-0.6475-0.3561-0.05260.29480.4956-0.4148-0.03750.4214-0.02630.07790.57430.07540.5354-3.113250.8339-27.238
208.6153-2.7865-7.7775.4713.85719.12920.2944-0.7923-0.07110.6587-0.0703-0.09610.0594-0.7768-0.34730.3189-0.0507-0.01090.55030.05930.2046-7.059247.3426-1.2933
212.4636-0.7013-0.18474.3581-4.13544.49470.71490.50380.8550.17830.11680.7429-2.67143.2104-0.11761.4326-0.4565-0.09231.1330.00741.023216.819864.8519-4.7362
222.6222-0.89910.25453.3189-2.49731.9167-0.1823-0.10050.09250.1728-0.1385-0.2638-1.51810.51010.23840.3334-0.0790.00350.30440.0030.42727.475457.7215-15.025
234.26662.72233.17863.55154.34675.442-0.33790.15250.39790.2543-0.09290.7343-2.0242-0.4190.24041.10560.3187-0.02130.35690.0080.4626-0.369762.8966-17.3791
246.22511.48264.36620.36671.21175.7132-0.2001-1.76851.78761.51440.089-0.1238-1.198-0.3446-0.08671.79140.1-0.08230.4452-0.38250.54722.476567.17875.6034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 6:49)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 50:76)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 77:103)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 104:121)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 24:64)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 65:85)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 86:106)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 107:120)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 31:41)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 42:65)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 66:80)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 81:121)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 14:32)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 33:65)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 66:93)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 94:121)
17X-RAY DIFFRACTION17(CHAIN E AND RESID 35:46)
18X-RAY DIFFRACTION18(CHAIN E AND RESID 47:65)
19X-RAY DIFFRACTION19(CHAIN E AND RESID 66:95)
20X-RAY DIFFRACTION20(CHAIN E AND RESID 96:120)
21X-RAY DIFFRACTION21(CHAIN F AND RESID 29:48)
22X-RAY DIFFRACTION22(CHAIN F AND RESID 49:89)
23X-RAY DIFFRACTION23(CHAIN F AND RESID 90:107)
24X-RAY DIFFRACTION24(CHAIN F AND RESID 108:120)

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