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- PDB-4ehy: Crystal structure of LpxK from Aquifex aeolicus in complex with A... -

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Basic information

Entry
Database: PDB / ID: 4ehy
TitleCrystal structure of LpxK from Aquifex aeolicus in complex with ADP/Mg2+ at 2.2 angstrom resolution
ComponentsTetraacyldisaccharide 4'-kinase
KeywordsTRANSFERASE / membrane protein / kinase / lipid A / P-loop / P-loop containing nucleoside triphosphate hydrolase / disaccharide-1-phosphate 4'-kinase / membrane / lipid metabolism / tetraacyldisaccharide 4'-kinase
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
ADENOSINE-5'-DIPHOSPHATE / Tetraacyldisaccharide 4'-kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.199 Å
AuthorsEmptage, R.P. / Daughtry, K.D. / Pemble IV, C.W. / Raetz, C.R.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface.
Authors: Emptage, R.P. / Daughtry, K.D. / Pemble, C.W. / Raetz, C.R.
History
DepositionApr 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: 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 / 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3617
Polymers36,5981
Non-polymers7636
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.110, 75.610, 104.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36597.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1656, lpxK / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: O67572, tetraacyldisaccharide 4'-kinase

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Non-polymers , 5 types, 73 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: sitting drop, vapor diffusion / pH: 7.5
Details: The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained 20% seed stock, ~1 mg/ml protein, 48% MPD, 80 mM Hepes pH 7.5, 4 mM Hepes pH 8.0, 130 mM NaCl, 3.4% ...Details: The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained 20% seed stock, ~1 mg/ml protein, 48% MPD, 80 mM Hepes pH 7.5, 4 mM Hepes pH 8.0, 130 mM NaCl, 3.4% glycerol, ~0.06% DDM, 1.8 mM ATP, 1.8 mM MgCl2, sutting drop, vapor diffusion, temperature 293K, sitting drop, vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. all: 26821 / Num. obs: 26285 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.049 / Χ2: 1.351 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.199-2.243.60.43411510.837186.9
2.24-2.283.90.39911830.91190.4
2.28-2.3240.36612750.887195
2.32-2.374.40.33712900.882199.1
2.37-2.424.60.28113060.852199.3
2.42-2.484.80.23813200.881100
2.48-2.544.90.20413200.8971100
2.54-2.614.90.17113320.8341100
2.61-2.6950.14113240.8781100
2.69-2.7750.12213140.8781100
2.77-2.874.90.0913320.946199.9
2.87-2.9950.07413191.016199.8
2.99-3.124.90.06813431.27199.9
3.12-3.294.90.05313271.268199.8
3.29-3.494.90.05113341.558199.7
3.49-3.764.90.0513531.998199.7
3.76-4.144.80.0513442.529199.3
4.14-4.744.80.0413572.874199
4.74-5.974.80.03413662.171198.6
5.97-504.50.02813952.087194.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å44.59 Å
Translation2.5 Å44.59 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EHX

4ehx


Resolution: 2.199→28.401 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 0.08 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 1999 8.13 %
Rwork0.1779 --
obs0.1808 24602 91.73 %
all-26285 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.768 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 170.39 Å2 / Biso mean: 65.3908 Å2 / Biso min: 24.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.2843 Å20 Å2-0 Å2
2--11.4845 Å20 Å2
3----11.2002 Å2
Refinement stepCycle: LAST / Resolution: 2.199→28.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 47 67 2634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082626
X-RAY DIFFRACTIONf_angle_d1.1573535
X-RAY DIFFRACTIONf_chiral_restr0.073380
X-RAY DIFFRACTIONf_plane_restr0.005438
X-RAY DIFFRACTIONf_dihedral_angle_d14.2991010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.199-2.25390.28651020.24971156125866
2.2539-2.31480.30291220.22851373149579
2.3148-2.38290.24841320.21081494162686
2.3829-2.45980.27181360.19941536167289
2.4598-2.54760.24881400.18721587172791
2.5476-2.64960.25771430.19171612175593
2.6496-2.77010.24851450.18561646179195
2.7701-2.9160.23691510.19051692184396
2.916-3.09840.2531480.19081680182897
3.0984-3.33730.23931530.17621735188898
3.3373-3.67260.20871550.17061746190199
3.6726-4.20250.20841540.15761751190599
4.2025-5.28910.17061580.15331774193299
5.2891-28.40370.19871600.19431821198196
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)
10.9625-0.30650.01290.7483-0.13580.02780.07880.38130.1578-0.1065-0.23380.4033-0.63260.0923-0.30310.65460.0305-0.08670.29470.12270.38994.54621.6629-21.6509
21.8003-0.0568-0.36861.3960.68374.81010.1438-0.5056-0.14230.03150.0724-0.20350.14671.1367-0.08150.34830.055-0.03970.53060.01960.40616.2098-12.4775-10.0093
31.6606-0.30990.94971.6208-0.55153.82720.0085-0.23850.0825-0.02570.08630.357-0.235-0.7171-0.07940.27150.03370.00730.35920.03020.4420.3911-6.1478-5.8146
42.03150.44380.98261.7307-0.16095.0108-0.0226-0.5670.01480.26430.17140.1946-0.2141-0.1783-0.06310.2797-0.00110.04750.39940.0030.34677.288-6.85525.7498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 8:50)A8 - 50
2X-RAY DIFFRACTION2chain 'A' and (resseq 51:130)A51 - 130
3X-RAY DIFFRACTION3chain 'A' and (resseq 131:228)A131 - 228
4X-RAY DIFFRACTION4chain 'A' and (resseq 229:315)A229 - 315

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