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- PDB-4itn: Crystal structure of "compact P-loop" LpxK from Aquifex aeolicus ... -

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Basic information

Entry
Database: PDB / ID: 4itn
TitleCrystal structure of "compact P-loop" LpxK from Aquifex aeolicus in complex with chloride 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
Tetraacyldisaccharide 4'-kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1912 Å
AuthorsEmptage, R.P. / Pemble IV, C.W. / York, J.D. / Raetz, C.R.H. / Zhou, P.
CitationJournal: Biochemistry / Year: 2013
Title: Mechanistic Characterization of the Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK Involved in Lipid A Biosynthesis.
Authors: Emptage, R.P. / Pemble, C.W. / York, J.D. / Raetz, C.R. / Zhou, P.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)37,2407
Polymers36,5981
Non-polymers6426
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.086, 68.524, 107.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: lpxK, aq_1656 / Production host: Escherichia coli (E. coli)
References: UniProt: O67572, tetraacyldisaccharide 4'-kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES, MPD, NaCl, DDM, Glycerol,methyl-2-acetamido-2-deoxy-B-D-glucopyranoside, 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.191→50 Å / Num. all: 24198 / Num. obs: 23573 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.046 / Χ2: 1.151 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.191-2.244.20.4519880.936183.4
2.24-2.284.60.38310580.956190
2.28-2.324.90.31711130.922192.8
2.32-2.375.30.29911420.906194.7
2.37-2.425.40.26411300.927197.7
2.42-2.485.50.21611830.965198.2
2.48-2.545.60.17711820.917198.9
2.54-2.615.60.16111890.9681100
2.61-2.695.70.14111991.0211100
2.69-2.775.80.12411940.9811100
2.77-2.875.80.09312011.0071100
2.87-2.995.70.07212021.041100
2.99-3.125.70.06212011.1091100
3.12-3.295.70.05112091.1841100
3.29-3.495.70.0511981.3871100
3.49-3.765.70.04812201.738199.9
3.76-4.145.60.04612202.065199.8
4.14-4.745.60.03612431.6131100
4.74-5.975.50.02912481.201199.9
5.97-505.20.0212530.853193.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EHX

4ehx


Resolution: 2.1912→26.197 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1121 5 %RANDOM
Rwork0.1927 ---
all0.1946 22403 --
obs0.1946 22403 92.48 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.243 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 167.85 Å2 / Biso mean: 71.5224 Å2 / Biso min: 24.59 Å2
Baniso -1Baniso -2Baniso -3
1-8.8616 Å2-0 Å2-0 Å2
2---4.3123 Å20 Å2
3----4.5493 Å2
Refinement stepCycle: LAST / Resolution: 2.1912→26.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 40 73 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082646
X-RAY DIFFRACTIONf_angle_d1.1633550
X-RAY DIFFRACTIONf_chiral_restr0.083383
X-RAY DIFFRACTIONf_plane_restr0.006443
X-RAY DIFFRACTIONf_dihedral_angle_d13.9191026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1912-2.29090.25861090.23252085219474
2.2909-2.41160.27841280.2152413254185
2.4116-2.56260.261380.21412630276892
2.5626-2.76020.26651420.22832691283395
2.7602-3.03760.2781460.21582764291097
3.0376-3.47630.2751490.20052843299299
3.4763-4.37650.22841520.17692886303899
4.3765-26.19930.18271570.17862970312798
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)
13.6074-3.45912.70133.5613-3.32744.23410.1651-0.2288-0.2649-0.85310.1696-0.02781.46820.1482-0.26820.87620.01870.05320.3548-0.05580.3676-0.7945-7.9541-27.3315
23.4693-0.72730.35033.7524-0.74085.74330.0725-0.3706-0.2350.27870.12460.622-0.153-0.4228-0.13460.3309-0.05890.16580.2659-0.02530.427-13.11259.5586-10.5014
31.71140.53850.69242.7739-0.14465.22130.365-0.2437-0.3190.2699-0.013-0.25770.19770.728-0.29170.2802-0.08030.02960.4419-0.09220.42361.07444.4653-6.7973
43.30330.8369-2.51530.3093-0.55275.3932-0.412-0.7426-0.7656-0.0114-0.1628-0.25170.72920.60890.47680.713-0.10380.15040.61630.06990.5878-6.27021.48426.3457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:26)A5 - 26
2X-RAY DIFFRACTION2chain 'A' and (resseq 27:130)A27 - 130
3X-RAY DIFFRACTION3chain 'A' and (resseq 131:231)A131 - 231
4X-RAY DIFFRACTION4chain 'A' and (resseq 232:315)A232 - 315

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