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- PDB-9cd1: Crystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-107 ... -

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Basic information

Entry
Database: PDB / ID: 9cd1
TitleCrystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-107 complex
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsANTIBIOTIC / LpxH / 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 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)30,3704
Polymers29,6281
Non-polymers7423
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.160, 106.160, 53.550
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-507-

HOH

21A-513-

HOH

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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-A1AVW / N-(4-{4-[6-chloro-4-(trifluoromethyl)pyridin-2-yl]piperazine-1-sulfonyl}phenyl)-2-[(methanesulfonyl)(methyl)amino]benzamide


Mass: 632.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25ClF3N5O5S2 / 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.: 129 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.91 mg/mL of LpxH, 0.1 mM LPH-107, 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 4.5, and 16 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2→46.27 Å / Num. obs: 23763 / % possible obs: 99.93 % / Redundancy: 10.2 % / Biso Wilson estimate: 26.68 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.52
Reflection shellResolution: 2→2.072 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 3.09 / Num. unique obs: 2345 / CC1/2: 0.858 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.27 Å / SU ML: 0.1756 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3972
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 1189 5 %
Rwork0.1941 22573 -
obs0.1949 23762 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.87 Å2
Refinement stepCycle: LAST / Resolution: 2→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 43 129 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022039
X-RAY DIFFRACTIONf_angle_d0.56962787
X-RAY DIFFRACTIONf_chiral_restr0.0419293
X-RAY DIFFRACTIONf_plane_restr0.0036365
X-RAY DIFFRACTIONf_dihedral_angle_d13.0937310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.24521470.22162799X-RAY DIFFRACTION99.97
2.09-2.20.19581460.20132767X-RAY DIFFRACTION99.93
2.2-2.340.2141480.18712809X-RAY DIFFRACTION100
2.34-2.520.23331470.19672797X-RAY DIFFRACTION100
2.52-2.770.20041480.18782811X-RAY DIFFRACTION99.97
2.77-3.170.23241480.22813X-RAY DIFFRACTION100
3.17-40.19971500.17932838X-RAY DIFFRACTION100
4-46.270.20051550.19992939X-RAY DIFFRACTION99.77
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)
11.74387826124-0.125305644190.4100197100851.7012422993-1.501252099232.638601982740.004574522148370.0846094360382-0.197938163809-0.33491865282-0.0580123442326-0.09973131966410.311394969497-0.03005360728820.06251909295410.2194098493090.01513066583460.01598504152570.17858330981-0.04090872124920.203168186386-36.6736200271-31.0798661215-1.04698605113
21.28864149561-0.644222657296-0.1830595459321.49679995067-0.1185842112670.553031612178-0.0153856087673-0.0634503313205-0.04844435024920.01921242851780.04279122606610.0807717903957-0.0461822438187-0.08743476501-0.02908149059760.186086217560.0220524584273-0.0195295121990.178054577994-0.01401628355640.173595012295-42.5407556249-23.66426308264.00311343852
32.657757117880.218920222372-0.4009177735262.72816200096-0.6722990893542.443999962660.000633364355647-0.3663044493850.06421182535050.256360123316-0.0246694496586-0.225152495139-0.05073630220480.1977932950530.06890661721080.1977986535420.0149750857825-0.003672658756860.214343209226-0.03047835554130.165344764444-32.5391652628-25.538988226212.8372710782
43.97114953904-2.207878107790.5027809119561.827482132480.2865616321861.76880747394-0.428805553765-0.8512048535970.6865364425130.4132507741920.383179061401-0.433596475290.0688767069030.0766036142428-0.01047976568430.3463710394080.0986642143096-0.07957403543780.287188803437-0.1000818430230.314025962517-38.1200754795-7.2790473234211.9989399584
53.31509273911.05484254824-2.961072095936.42441156665-1.204842077968.17675039434-0.5396851816950.5245275670310.210879301061-1.483504415270.00714801641708-0.849639449611-0.5789807981950.08274807796020.4035620816340.492413606541-0.02388770063290.03596891404820.197111333508-0.04825526680650.406915286405-42.5040134979-5.09422340502-1.00113745624
65.78523562295-1.81914892566-0.07788806080374.564423487690.20105873911.68988018022-0.174515016721-0.2703888210261.05064215460.403169425050.0853581285694-0.422069394655-0.2721921169630.4466615308780.1502179997380.289792993484-0.0246647655056-0.07404917804260.320290515355-0.08756306007940.437265940809-18.2403417436-19.11131982613.2937684267
73.9619574318-0.345335839248-0.1339060209012.267611958170.8417599790562.5641819293-0.00507613586193-0.07144390338830.09801875435750.03461707667470.052944672312-0.2961365459410.007524180876950.103319828436-0.04798994968480.1649899980040.00446890960306-0.006522120443660.167430981876-0.01225422463130.212016280794-21.0683307957-28.74598925316.8262238374
81.23329669414-0.570702010629-0.3294300059961.369719158391.770350461413.815697291660.2465337508580.479656558295-0.194045990526-0.449617520407-0.3027346919060.100598597491-0.04877973991890.1173359853870.0628078238170.3402379191720.089861110679-0.03745189176250.329044230046-0.04264969488250.352817758919-26.6257478817-39.2166880278-10.3750553409
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 159 )146 - 159145 - 158
66chain 'A' and (resid 160 through 185 )160 - 185159 - 174
77chain 'A' and (resid 186 through 228 )186 - 228175 - 217
88chain 'A' and (resid 229 through 252 )229 - 252218 - 239

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