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- PDB-9ccx: Crystal Structure of the Klebsiella pneumoniae LpxH/JH-LPH-86 complex -

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Basic information

Entry
Database: PDB / ID: 9ccx
TitleCrystal Structure of the Klebsiella pneumoniae LpxH/JH-LPH-86 complex
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsANTIBIOTIC / LpxH / Inhibitor / Complex / Lipid A
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: 2.3 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)30,3865
Polymers29,6281
Non-polymers7594
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.630, 106.630, 54.270
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-A1AVZ / 1-(5-{4-[4-(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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 mg/mL of LpxH, 0.14 mM LPH-86, 10 mM MES (pH 6.0), 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 0.8% DMSO, 0.05 M sodium acetate pH 5.0, and 18 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→46.79 Å / Num. obs: 15953 / % possible obs: 99.15 % / Redundancy: 8 % / Biso Wilson estimate: 42.44 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.56
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1564 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.79 Å / SU ML: 0.2258 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 796 5 %
Rwork0.1941 15135 -
obs0.1958 15931 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 46 41 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542012
X-RAY DIFFRACTIONf_angle_d0.70862744
X-RAY DIFFRACTIONf_chiral_restr0.0521294
X-RAY DIFFRACTIONf_plane_restr0.0064353
X-RAY DIFFRACTIONf_dihedral_angle_d16.2742311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.32371300.27012487X-RAY DIFFRACTION99.62
2.44-2.630.35181300.25842489X-RAY DIFFRACTION99.36
2.63-2.90.22881330.20112510X-RAY DIFFRACTION99.36
2.9-3.320.2271340.19292539X-RAY DIFFRACTION99.66
3.32-4.180.21631330.17282534X-RAY DIFFRACTION99.4
4.18-46.790.19841360.1842576X-RAY DIFFRACTION97.62
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)
12.03717426394-0.8067666718041.457943970462.59523716583-2.300595323854.316621211860.07078984631450.122321344809-0.0809750649228-0.222884238534-0.138197375378-0.09236716633760.2127493283640.203125113550.1329695049340.3802369597210.0160383041684-0.002487761196510.364290154478-0.02998127413350.324686522786-36.86439912-31.1560613845-0.781545003113
21.90271275254-0.220250680347-0.3914083474672.27034086634-0.3120580568061.41680905933-0.01519428919-0.1951554799170.1229489562680.09540760478290.0126876888547-0.252217467218-0.01900752392780.0314048217818-0.00602666215390.3309632999460.01415149674930.009148212155850.362869238584-0.03027094813610.316687541559-37.9038005512-24.63005076988.06329678043
32.59232848372-1.11519794995-0.04304172507692.574790711220.6334711295381.86608089401-0.114525344903-0.06762619663630.00111606397708-0.0654371657530.100981215343-0.156094812649-0.1847811592920.02271773870910.01887990508910.432028297970.0115425764149-0.02690635102740.337519650109-0.09549732913220.494662067834-38.7175291895-6.182544723095.99514959622
44.06333564992-3.464592642561.586647444028.13660526975-1.251135439940.6211551070220.0492810546044-0.2125130035550.8086663294060.460525616144-0.38882123179-1.12536285992-0.2668909931350.08694550480610.3282512431320.4157946116680.0242275182324-0.03789682868670.582504077173-0.07105729567270.641518697247-18.4624873403-18.786671728812.5528858315
52.84004480486-0.0502520250135-0.7516527808022.68503864331.234396802752.341921273060.0248005201618-0.05594673119110.1975896834820.1286775393940.121355804246-0.3288056943690.008905522310970.102336312659-0.1534552144480.3063986186780.00653712493153-0.039311956140.317046828573-0.02412615304780.379348354998-21.3834565416-29.06560818577.49858573761
61.24885053737-0.1542493955350.4547923944911.47147219511.183132551673.510672868210.1312179061830.4100929144410.192246516195-0.472248142979-0.2083698803110.1659440207020.2384528942850.06806243797770.04678964415430.4962028117650.0312868317732-0.006488383719980.5187453235020.04496878638020.574357120194-26.7108647778-40.0090825946-12.033973967
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 122 )39 - 12238 - 121
33chain 'A' and (resid 123 through 162 )123 - 162122 - 161
44chain 'A' and (resid 163 through 185 )163 - 185162 - 177
55chain 'A' and (resid 186 through 228 )186 - 228178 - 220
66chain 'A' and (resid 229 through 252 )229 - 252221 - 244

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