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- PDB-4lkv: Determinants of lipid substrate and membrane binding for the tetr... -

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Basic information

Entry
Database: PDB / ID: 4lkv
TitleDeterminants of lipid substrate and membrane binding for the tetraacyldisaccharide-1-phosphate 4 -kinase LpxK
ComponentsTetraacyldisaccharide 4'-kinase
KeywordsTRANSFERASE / P-loop containing nucleotide triphosphate hydrolase / Kinase / Membrane Protein
Function / homology
Function and homology information


tetraacyldisaccharide 4'-kinase / tetraacyldisaccharide 4'-kinase activity / lipopolysaccharide core region biosynthetic process / lipid A biosynthetic process / phosphorylation / ATP binding / plasma membrane
Similarity search - Function
Tetraacyldisaccharide 4'-kinase / Tetraacyldisaccharide-1-P 4'-kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-LP4 / Chem-LP5 / Tetraacyldisaccharide 4'-kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.5109 Å
AuthorsEmptage, R.P. / Tonthat, N.K. / York, J.D. / Schumacher, M.A. / Zhou, P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis of Lipid Binding for the Membrane-embedded Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK.
Authors: Emptage, R.P. / Tonthat, N.K. / York, J.D. / Schumacher, M.A. / Zhou, P.
History
DepositionJul 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Sep 24, 2014Group: Database references
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Tetraacyldisaccharide 4'-kinase
B: Tetraacyldisaccharide 4'-kinase
C: Tetraacyldisaccharide 4'-kinase
D: Tetraacyldisaccharide 4'-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,4779
Polymers146,3914
Non-polymers3,0865
Water0
1
A: Tetraacyldisaccharide 4'-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2604
Polymers36,5981
Non-polymers1,6623
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tetraacyldisaccharide 4'-kinase


Theoretical massNumber of molelcules
Total (without water)36,5981
Polymers36,5981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tetraacyldisaccharide 4'-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0213
Polymers36,5981
Non-polymers1,4242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tetraacyldisaccharide 4'-kinase


Theoretical massNumber of molelcules
Total (without water)36,5981
Polymers36,5981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.632, 140.691, 173.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain D) / NCS domain segments: (Selection details: chain 'D')
DetailsEstimated from size exclusion chromatography and asymmetric unit of entries 4EHW, 4EHX, and 4EHY.

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Components

#1: Protein
Tetraacyldisaccharide 4'-kinase / / Lipid A 4'-kinase


Mass: 36597.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: lpxK, aq_1656 / Production host: Escherichia coli (E. coli)
References: UniProt: O67572, tetraacyldisaccharide 4'-kinase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-LP4 / 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#4: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
Nonpolymer detailsLIPID IVa is represented by LP4 AND LP5

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES, MPD, lipid IVa, Tris, Triton X-100, DDM, NaCl, MgCl2, ADP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2012
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 21311 / Num. obs: 20053 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.565.70.6872174.2
3.56-3.636.90.6632.4177.3
3.63-3.698.50.5613.4178.6
3.69-3.779.10.5083.8183.7
3.77-3.8510.50.4615184.5
3.85-3.9411.10.4086190.1
3.94-4.0411.90.3826.9196.3
4.04-4.1512.70.3458.5199.6
4.15-4.2713.90.26812.31100
4.27-4.4114.60.21815.51100
4.41-4.5714.90.16819.11100
4.57-4.7515.10.14421.81100
4.75-4.97150.14221.71100
4.97-5.23150.13522.91100
5.23-5.5514.90.12923.91100
5.55-5.9814.80.11824.21100
5.98-6.5814.80.125.91100
6.58-7.5314.70.08626.91100
7.53-9.4814.30.08126.61100
9.48-5012.40.08922.4196.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementResolution: 3.5109→39.51 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.51 / σ(F): 0.17 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3305 1790 9.99 %
Rwork0.2667 --
obs0.273 17918 84.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 185.5541 Å2
Refinement stepCycle: LAST / Resolution: 3.5109→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10257 0 109 0 10366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810592
X-RAY DIFFRACTIONf_angle_d0.83314250
X-RAY DIFFRACTIONf_dihedral_angle_d13.244107
X-RAY DIFFRACTIONf_chiral_restr0.0381559
X-RAY DIFFRACTIONf_plane_restr0.0041786
Refine LS restraints NCSNumber: 6212 / Type: POSITIONAL / Rms dev position: 8.986 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5109-3.60580.3973590.3262548X-RAY DIFFRACTION38
3.6058-3.71180.4044820.3343800X-RAY DIFFRACTION55
3.7118-3.83150.38231080.3151957X-RAY DIFFRACTION66
3.8315-3.96830.41521260.30831057X-RAY DIFFRACTION73
3.9683-4.12710.361310.29061156X-RAY DIFFRACTION80
4.1271-4.31470.31081450.27641329X-RAY DIFFRACTION91
4.3147-4.54180.30481620.26461427X-RAY DIFFRACTION97
4.5418-4.82590.29361540.24291431X-RAY DIFFRACTION98
4.8259-5.19780.32511700.25051449X-RAY DIFFRACTION98
5.1978-5.71950.37781610.27431469X-RAY DIFFRACTION99
5.7195-6.54390.39391600.30871483X-RAY DIFFRACTION99
6.5439-8.23230.33611610.27781500X-RAY DIFFRACTION100
8.2323-39.51230.25841710.20521522X-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)
10.054-0.01470.0870.0069-0.03280.1451-0.23370.090.3471-0.0985-0.2026-0.1159-0.3003-0.1415-1.26120.37820.2283-0.19050.17690.15550.4117-56.1398-7.3224-34.7332
20.60720.055-0.19580.67230.42330.3704-0.2274-0.20760.13080.1718-0.1936-0.1555-0.0548-0.0729-1.44940.28640.0913-0.13470.39290.09060.082-53.4395-12.2966-14.753
30.6063-0.03470.25890.4326-0.30580.6645-0.4692-0.18680.26180.1666-0.3672-0.4204-0.04240.139-4.9141-0.3450.40560.06850.29530.2410.0942-52.2473-12.1031-21.9327
40.25920.1239-0.04240.13490.08850.33810.03340.007-0.2280.06080.18740.00980.37720.18810.16570.13020.2344-0.33340.72850.47410.8635-44.1748-32.1921-15.9117
50.9047-0.4468-0.01840.23850.07750.1664-0.0202-0.2489-0.52970.0563-0.10850.17410.1343-0.0957-0.70120.23780.0688-0.30690.6150.28870.9226-49.663-27.8909-13.6057
60.01050.0242-0.01420.2141-0.23520.91-0.00940.0551-0.2144-0.0523-0.12210.08910.4743-0.213-0.41950.2516-0.14140.087-0.0437-0.29480.7928-10.1635-57.921-35.9536
70.061-0.16570.08660.5145-0.15020.295-0.16360.01730.05140.2164-0.2107-0.0055-0.14850.1372-0.65070.2717-0.37530.22780.4381-0.18170.7914-12.6376-51.8261-16.1243
80.01610.04760.02430.16980.07940.0346-0.0634-0.0761-0.15320.2843-0.01070.23860.1115-0.0466-0.08810.4249-0.01320.06940.0732-0.04350.6135-5.8371-53.7141-11.8167
90.0172-0.0427-0.04090.13710.10030.08470.06440.3156-0.35380.0321-0.23720.49860.0466-0.3775-0.05290.1501-0.2751-0.01530.1694-0.62040.6242-18.7177-47.6198-27.1284
100.1079-0.0227-0.06970.00640.01910.0487-0.01910.05490.0505-0.01520.02210.0245-0.02180.01230.08750.1022-0.16520.08250.2804-0.31510.312-10.3823-26.1424-21.9355
110.7079-0.13480.13560.38490.04480.3210.0128-0.0731-0.26970.2307-0.09790.15210.0453-0.22590.02250.1304-0.16290.06090.3633-0.36570.4539-11.2459-37.0716-16.5079
120.0099-0.04480.0770.1815-0.30950.54730.09560.0345-0.3314-0.12790.0820.53730.0917-0.25670.13080.25730.0587-0.11620.211-0.03150.5641-24.505722.2069-3.8299
130.2711-0.00710.03850.00080.0060.0105-0.00240.2022-0.0229-0.38660.11490.09730.0688-0.05610.5881.2252-0.4478-0.22010.2895-0.12380.0447-20.43029.5667-23.8425
140.1339-0.0601-0.04670.04310.11620.5658-0.0510.13640.0519-0.2704-0.0614-0.025-0.1795-0.0819-0.33051.7115-0.33790.02690.6175-0.09490.1425-17.983114.1359-34.2292
150.11220.0635-0.16050.0774-0.11090.22350.0746-0.0551-0.03850.01730.27970.20620.25110.06152.33271.3543-0.1418-0.24350.14490.2194-0.235-18.14778.1083-11.9281
161.1256-0.05130.36610.09670.38251.98550.06430.4112-0.0933-0.29340.3165-0.4015-0.3390.8122-0.03220.8736-0.06140.07610.4103-0.22130.30383.68585.1352-24.8646
170.01110.00550.00150.0171-0.00780.0039-0.0883-0.00390.1068-0.04970.05830.13180.01110.0023-01.1701-0.0579-0.11811.0989-0.27181.5425.289718.4295-18.8111
180.02170.01040.02260.00620.0150.0276-0.21460.32280.1902-0.15390.02170.0183-0.0211-0.40690.00910.6408-0.2978-0.39411.35170.27191.28525.617125.6312-26.6905
190.3999-0.02080.13320.4346-0.28110.2160.23220.40260.3105-0.60070.3629-0.2864-0.39920.57260.14941.1194-0.28840.42730.7243-0.27380.9452-3.7987.1171-27.0936
200.0129-0.01580.0108-0.03150.01350.0014-0.2546-0.43170.11030.5634-0.18830.5180.45120.0956-1.18521.01980.78881.2040.7244-0.44220.688-36.1475-26.2055-62.7862
210.2659-0.04570.04020.0167-0.02150.04690.07760.17040.142-0.1134-0.2370.0123-0.0538-0.0294-0.27670.52230.20660.31760.43510.04820.5988-33.986-14.3567-75.8878
220.15120.09480.15720.2914-0.10.3010.0475-0.2550.0790.02210.03480.1603-0.0850.07030.31320.70980.2380.34820.7445-0.23210.6848-21.2199-10.6826-57.8599
230.04040.0085-0.01190.0248-0.02430.02280.1584-0.24520.21930.10810.25930.0546-0.13070.302200.7801-0.00450.17920.5547-0.02530.709-7.5692-17.0779-61.1806
240.10960.0172-0.08130.0937-0.00360.0648-0.0499-0.3263-0.06160.2129-0.01760.11790.07250.03010.17910.37760.20640.24961.0928-0.08480.3657-8.7252-25.2858-53.6399
250.49890.0592-0.02090.0699-0.08140.11750.11290.10540.25150.1006-0.19340.4832-0.1178-0.232-0.11731.06830.41210.19990.8061-0.26361.06-34.4234-8.5216-60.9394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 248 )
5X-RAY DIFFRACTION5chain 'A' and (resid 249 through 315 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 50 )
7X-RAY DIFFRACTION7chain 'B' and (resid 51 through 80 )
8X-RAY DIFFRACTION8chain 'B' and (resid 81 through 129 )
9X-RAY DIFFRACTION9chain 'B' and (resid 130 through 222 )
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 248 )
11X-RAY DIFFRACTION11chain 'B' and (resid 249 through 315 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 25 )
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 80 )
14X-RAY DIFFRACTION14chain 'C' and (resid 81 through 129 )
15X-RAY DIFFRACTION15chain 'C' and (resid 130 through 199 )
16X-RAY DIFFRACTION16chain 'C' and (resid 200 through 228 )
17X-RAY DIFFRACTION17chain 'C' and (resid 229 through 248 )
18X-RAY DIFFRACTION18chain 'C' and (resid 249 through 267 )
19X-RAY DIFFRACTION19chain 'C' and (resid 268 through 315 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 173 )
21X-RAY DIFFRACTION21chain 'D' and (resid 174 through 199 )
22X-RAY DIFFRACTION22chain 'D' and (resid 200 through 221 )
23X-RAY DIFFRACTION23chain 'D' and (resid 222 through 248 )
24X-RAY DIFFRACTION24chain 'D' and (resid 249 through 290 )
25X-RAY DIFFRACTION25chain 'D' and (resid 291 through 315 )

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