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- PDB-6wii: Crystal structure of the K. pneumoniae LpxH/JH-LPH-41 complex -

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Basic information

Entry
Database: PDB / ID: 6wii
TitleCrystal structure of the K. pneumoniae LpxH/JH-LPH-41 complex
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / LpxH / JH-LPH-41 / Lipid A / Antibiotic
Function / homology
Function and homology information


UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / lipid A biosynthetic process / extrinsic component of plasma membrane / manganese ion binding / cytoplasm
Similarity search - Function
UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase LpxH-like / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / Chem-U2V / UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCochrane, C.S. / Cho, J. / Fenton, B.A. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139216 United States
CitationJournal: Bioorg.Chem. / Year: 2020
Title: Synthesis and evaluation of sulfonyl piperazine LpxH inhibitors.
Authors: Kwak, S.H. / Cochrane, C.S. / Ennis, A.F. / Lim, W.Y. / Webster, C.G. / Cho, J. / Fenton, B.A. / Zhou, P. / Hong, J.
History
DepositionApr 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6428
Polymers29,6281
Non-polymers1,0147
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.710, 105.710, 53.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-535-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-2,3-diacylglucosamine hydrolase / UDP-2 / 3-diacylglucosamine diphosphatase


Mass: 29627.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: lpxH_1, lpxH, C3483_19950, NCTC9128_00880, SAMEA104305404_03891
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1S0WIC1, UniProt: A6T5R0*PLUS, UDP-2,3-diacylglucosamine diphosphatase

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-U2V / 5-({[4-({4-[3-chloro-5-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)phenyl]carbamoyl}amino)-N-hydroxypentanamide


Mass: 578.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27ClF3N5O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 4 mg/mL of LpxH, 0.27 mM JH-LPH-41, 10 mM MES (pH 6.0), 100 mM NaCl, 100 mM KCl, 50 mM sodium citrate (pH 5.5), 18.5% pentaerythritol propoxylate (5/4 PO/OH), 0.5mM DTT, 1% DMSO, 2.5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→46.29 Å / Num. obs: 29725 / % possible obs: 99.9 % / Redundancy: 10.97 % / Biso Wilson estimate: 26.34 Å2 / Rrim(I) all: 0.092 / Net I/σ(I): 16.88
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 2156 / Rrim(I) all: 0.863

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PJ3

6pj3


Resolution: 1.85→45.77 Å / SU ML: 0.1555 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.3007
RfactorNum. reflection% reflection
Rfree0.187 1486 5 %
Rwork0.1603 --
obs0.1616 29704 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 58 152 2091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662074
X-RAY DIFFRACTIONf_angle_d0.8632831
X-RAY DIFFRACTIONf_chiral_restr0.0561299
X-RAY DIFFRACTIONf_plane_restr0.0058369
X-RAY DIFFRACTIONf_dihedral_angle_d20.6312740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.19811340.18722536X-RAY DIFFRACTION99.96
1.91-1.980.19381330.16882529X-RAY DIFFRACTION100
1.98-2.060.17131340.15452539X-RAY DIFFRACTION100
2.06-2.150.18541340.15022545X-RAY DIFFRACTION99.33
2.15-2.260.19281320.15082511X-RAY DIFFRACTION100
2.26-2.410.15921350.15412573X-RAY DIFFRACTION99.96
2.41-2.590.19821350.16842556X-RAY DIFFRACTION100
2.59-2.850.21671360.16572577X-RAY DIFFRACTION100
2.85-3.260.18381350.16392569X-RAY DIFFRACTION100
3.27-4.110.17121370.14232595X-RAY DIFFRACTION99.85
4.11-45.770.19381410.17122688X-RAY DIFFRACTION99.93
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)
10.4347528077210.559484083397-0.08726321930310.624378144033-0.1372509814040.4748543409670.01268522988780.227238100887-0.0104819408595-0.122121922321-0.0562022466086-0.1092657656740.08687026053970.08810243532698.40153129761E-50.1968548699960.02143083249920.006981255784450.235824582687-0.0181902127610.1882383509968.5365960986-46.8840888692-10.011699734
20.4613347445160.366280507887-0.129058818710.2555908807790.2082525921620.235479844137-0.005689359792310.01646878583520.001529846484060.0305342686375-0.02706025287490.04546316903490.0300821432086-0.111895734499-4.0564279228E-50.1915430338030.00356396991782-0.003165514209040.23159991455-0.02047300019320.208277196598-0.77192754475-48.6041899622-5.31071749082
30.297733376619-0.18142463210.06340561341180.396223157341-0.462292448180.5148236030620.0251703740655-0.398985237927-0.09627323643090.129872511281-0.1171250092170.0599740052223-0.0377768953256-0.0637413440838-5.27203167347E-50.23223895087-0.0229940342620.01853962463580.290834166435-0.01410865522260.2192140294693.44856597173-47.14677596494.23593494785
40.1264940639190.178061856373-0.2094374511490.134715236818-0.1540695754810.497632722906-0.0247945635686-0.1795691507760.3230016096880.202632737126-0.000282471468566-0.114354708154-0.2324922300670.03270477346490.0001414472890420.257602493712-0.0191791807837-0.01539434296380.243160055132-0.05407430983280.3046086815578.86394267378-33.14143808753.39999532641
50.436133156184-0.03768942413440.2714183622190.5182599156770.07873625391.058972143960.334913355743-0.7229191209470.5319296522810.357802486856-0.451405152910.3804347886380.22117232213-0.1337949517180.3086210041540.161468655759-0.03466826398240.05845551377950.366936611208-0.1493483392980.327744335636-12.8058513663-36.41191337132.94690923822
60.127592161573-0.2085472519290.0001680759237840.213479686197-0.08864120896180.1397861458220.1321767529040.3926658918510.143130340384-0.520038902803-0.558639079385-0.153664715287-0.114829001151-0.114251468939-0.01194482963210.2653639668670.06456871299170.02635196415350.371814145766-0.02742792008460.31963730317-16.3520587859-40.2489072504-10.3087934547
71.116011096450.766815244264-0.5931474728110.859908192859-0.4807978041680.4865462635050.0592641471173-0.04354219009990.292841021952-0.01430589646310.04220491753250.0427665409328-0.1054389065920.05250892970460.0001309987353350.208766938637-0.0148279728361-0.009374844427110.227051473928-0.04532160322690.25994731472312.489245767-30.7951342632-0.502304422299
80.388216035098-0.210684363532-0.2464452697160.3464634904220.1208031100160.10686535993-0.04977789335930.0777811436239-0.1325516983890.0131233958417-0.0384876138477-0.006395800565480.00453795218-0.005949955888348.66052783516E-70.189926914449-0.03189959584660.001085262778850.324677486038-0.02056939071710.23761748001919.5250484173-43.251178772-17.6997411064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 145 )
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 158 )
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 228 )
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 249 )

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