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- PDB-9ccy: Crystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-90 c... -

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Basic information

Entry
Database: PDB / ID: 9ccy
TitleCrystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-90 complex
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsANTIBIOTIC / LpxH / lipid A / inhibitor
Function / homology
Function and homology information


UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / extrinsic component of plasma membrane / lipid A biosynthetic process / 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
: / : / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCochrane, C.S. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Jacs Au / Year: 2024
Title: Design and Evaluation of Pyridinyl Sulfonyl Piperazine LpxH Inhibitors with Potent Antibiotic Activity Against Enterobacterales.
Authors: Ennis, A.F. / Cochrane, C.S. / Dome, P.A. / Jeong, P. / Yu, J. / Lee, H. / Williams, C.S. / Ha, Y. / Yang, W. / Zhou, P. / Hong, J.
History
DepositionJun 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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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)30,1924
Polymers29,6281
Non-polymers5643
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.710, 105.710, 53.560
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

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Components

#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, UDP-2,3-diacylglucosamine diphosphatase
#2: Chemical ChemComp-A1AVY / 1-(5-{4-[6-(trifluoromethyl)pyridin-2-yl]piperazine-1-sulfonyl}-2,3-dihydro-1H-indol-1-yl)ethan-1-one


Mass: 454.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21F3N4O3S / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 57.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2 mg/mL of LpxH, 0.16 mM LPH-90, 10 mM MES (pH 6.0), 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 0.8% DMSO, 0.05 M HEPES pH 7.0, and 18 % w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953738 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953738 Å / Relative weight: 1
ReflectionResolution: 2.05→45.77 Å / Num. obs: 21766 / % possible obs: 99.29 % / Redundancy: 20 % / Biso Wilson estimate: 38.47 Å2 / CC1/2: 1 / Net I/σ(I): 22.75
Reflection shellResolution: 2.05→2.123 Å / Num. unique obs: 2159 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→45.77 Å / SU ML: 0.1856 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.7535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 1089 5 %
Rwork0.1846 20673 -
obs0.1858 21762 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.99 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 33 85 2038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392025
X-RAY DIFFRACTIONf_angle_d0.6352761
X-RAY DIFFRACTIONf_chiral_restr0.0467294
X-RAY DIFFRACTIONf_plane_restr0.0055358
X-RAY DIFFRACTIONf_dihedral_angle_d10.7183306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.140.25591350.19872569X-RAY DIFFRACTION99.89
2.14-2.260.20471360.19342563X-RAY DIFFRACTION99.89
2.26-2.40.23111340.17482562X-RAY DIFFRACTION99.96
2.4-2.580.22221370.18712596X-RAY DIFFRACTION100
2.58-2.840.22961360.19262588X-RAY DIFFRACTION99.96
2.84-3.250.19611370.19082592X-RAY DIFFRACTION100
3.25-4.10.21541310.17412501X-RAY DIFFRACTION94.95
4.1-45.770.19441430.18572702X-RAY DIFFRACTION99.96
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)
11.719296033-0.4142477544510.3439063505091.93961494584-1.561099985982.524778012940.02912426904830.147595795706-0.154916949088-0.399835500378-0.177760440004-0.1539778769390.2845674721350.079341405820.130235924380.3707256648410.00990289447189-0.02155848482860.352003392782-0.02695032186490.334746016762-36.3525615033-30.8847221423-1.04164616212
21.03559763449-1.058038021880.02175928523891.32023650401-0.1970129430660.586617613877-0.0279377548581-0.1053353615250.112939457880.007338047398460.04467584416760.0102526448721-0.0867535947579-0.0202971376158-0.01723529338820.3396203103680.00883817935684-0.01322046384550.335493455049-0.02167221584750.337024153037-42.1860294773-23.35771181644.0206210601
31.923372238210.318274913606-0.3565561796851.47534656379-0.4443444186441.42653506043-0.0414537878614-0.3512349311140.09274976003130.2643616777910.00411813614801-0.137416326375-0.0002021838818350.1875551864260.04287253833060.3551658675840.0156747086087-0.01128055382960.411855547486-0.02489153556260.333099288806-32.1395686954-25.802005125412.8346074888
42.45610493604-0.863537942260.2055983637671.804996835320.5717544812161.64943687541-0.287441489936-0.6839698098240.5819607406550.4429945111360.277628018793-0.552545928750.04702475385870.1400194705230.01865577247090.4387172192450.0302401478783-0.07690178791030.414539286084-0.124591328290.534845954401-37.0643935657-6.9349783165911.4919931968
55.097730535550.386817133251-1.089507052964.2625492867-0.2494443928513.93230557866-0.03490624565040.493103693736-0.0603182672846-1.10822687303-0.143234475392-0.258737243608-0.1675657282370.3017827536390.1436086780190.5963453994570.02644271445810.01545677610420.383245958287-0.05250635987270.474612063428-41.0156813738-5.02989385667-1.49518467578
63.23184096748-1.766574883570.5377971398334.69425427896-0.1377819922320.137947129649-0.272184198624-0.4116020273260.6272446034050.512509699952-0.0297134923295-0.963690214547-0.2820607497810.08882868873830.2054855420090.367126046701-0.0322430148497-0.06076704678210.509908788997-0.05067438992140.50193640066-18.5082559586-18.526846641912.0041168749
72.266217124470.282560659033-0.8008201242291.894223666830.7216710906821.70996843540.0243166935921-0.04790100580470.1101718900260.0441808245168-0.00712997795624-0.4560442271440.06560253282860.130651340770.002777724862070.3195847755780.0356090303963-0.05810571834690.379637412388-0.01855504836150.412837484274-20.814777744-28.49430102077.26768958545
80.649013336435-0.363689623577-0.2453033481781.230085395441.276044119271.300001152850.1511093139710.300952974842-0.0932828063978-0.453537159571-0.2007630898870.2078343692750.00408745031354-0.03359990820310.008053393544870.4804892082480.0752458219408-0.04730900225690.471085811109-0.01852485314550.434653816226-26.5882811219-38.8932249162-10.4007109906
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 38 )2 - 381 - 37
22chain 'A' and (resid 39 through 85 )39 - 8538 - 84
33chain 'A' and (resid 86 through 122 )86 - 12285 - 121
44chain 'A' and (resid 123 through 145 )123 - 145122 - 144
55chain 'A' and (resid 146 through 161 )146 - 161145 - 160
66chain 'A' and (resid 162 through 185 )162 - 185161 - 177
77chain 'A' and (resid 186 through 228 )186 - 228178 - 220
88chain 'A' and (resid 229 through 252 )229 - 252221 - 242

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