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- PDB-9cd0: Crystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-106 ... -

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Basic information

Entry
Database: PDB / ID: 9cd0
TitleCrystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-106 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
: / : / DI(HYDROXYETHYL)ETHER / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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)30,6086
Polymers29,6281
Non-polymers9805
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
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-440-

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-A1AVX / N-[2-(5-{4-[6-chloro-4-(trifluoromethyl)pyridin-2-yl]piperazine-1-sulfonyl}-2,3-dihydro-1H-indole-1-carbonyl)phenyl]-N-methylmethanesulfonamide


Mass: 658.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27ClF3N5O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 205 / 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: 1.1 mg/mL of LpxH, 0.15 mM LPH-106, 10 mM MES (pH 6.0), 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 0.8% DMSO, 0.05 M HEPES pH 6.5, and 18 % w/v PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.72→45.97 Å / Num. obs: 36785 / % possible obs: 98.96 % / Redundancy: 9.9 % / Biso Wilson estimate: 19.98 Å2 / CC1/2: 0.981 / Net I/σ(I): 6.99
Reflection shellResolution: 1.72→1.782 Å / Num. unique obs: 3659 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→45.97 Å / SU ML: 0.1866 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 1837 5 %
Rwork0.181 34934 -
obs0.1826 36771 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.26 Å2
Refinement stepCycle: LAST / Resolution: 1.72→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 59 205 2195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01612136
X-RAY DIFFRACTIONf_angle_d1.35742918
X-RAY DIFFRACTIONf_chiral_restr0.097301
X-RAY DIFFRACTIONf_plane_restr0.013382
X-RAY DIFFRACTIONf_dihedral_angle_d20.2586336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.770.2761410.22792678X-RAY DIFFRACTION99.93
1.77-1.820.24011410.19872671X-RAY DIFFRACTION100
1.82-1.880.21281420.18242703X-RAY DIFFRACTION100
1.88-1.940.35151320.30032492X-RAY DIFFRACTION92.95
1.94-2.020.23821420.1852694X-RAY DIFFRACTION100
2.02-2.110.2541400.19642676X-RAY DIFFRACTION99.36
2.11-2.230.22311420.17032695X-RAY DIFFRACTION99.75
2.23-2.360.24531360.21212583X-RAY DIFFRACTION95.14
2.37-2.550.20811430.16892714X-RAY DIFFRACTION100
2.55-2.80.19051430.1642724X-RAY DIFFRACTION100
2.8-3.210.21921430.17682725X-RAY DIFFRACTION100
3.21-4.040.18181430.15742727X-RAY DIFFRACTION99.51
4.05-45.970.18151490.1762852X-RAY DIFFRACTION100
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)
13.106993664920.218816997859-2.216171842622.543482134760.2459411157724.432897935810.03143825775520.3211683350860.125546120219-0.152470870242-0.04910217688560.164217472468-0.107841482449-0.19370880650.01180792831790.107643383854-0.00256412998687-0.04396776259540.1669145282440.003437143574730.144087835735-8.5758751177747.2511053173-9.95077222892
22.339637595740.179572808495-0.1245233677181.470450123950.1009641796391.259710886670.0479428363978-0.08524285863110.01526002418490.117802366007-0.0447656284717-0.008737750890650.0292200281366-0.00321689345718-0.003498214506070.11796369078-0.0058534704203-0.01485162184920.135162470099-0.0007271122420970.118929252546-2.6388526575844.8357577981-0.794788470465
34.006327819012.87261659247-0.389964593913.72821886716-0.9266676029381.239422953940.241221787096-0.414514666335-0.4612990778530.26616497257-0.217264151476-0.1416993033160.09632504223720.0207968669126-0.01610535624360.16941141340.0067794276215-0.05028708182790.2239567091060.05768825489090.25151561691812.665820367935.8403301052.71157304609
45.890895047843.684175533311.849051160256.686590613393.528657420567.923173495960.000306160255540.507837619562-0.412212938466-0.311009173081-0.180091955367-0.192256959590.1852457988770.008841524135450.1795195593390.1707478104680.0699288322333-0.009119065532670.2765736774920.01345531363940.24119459600116.02231800238.4352068312-10.4013590631
55.74772319981-0.328406398153-0.680960857853.857783985160.2607749460022.660135520270.0252426545464-0.436336711529-0.719102139470.265018149553-0.0244701182379-0.133431170690.467070960940.0881868126680.06132525877330.213948972527-0.0168223116872-0.06211766142590.1970502613130.07875483310190.255542175351-7.2309021880425.25973210863.6285895746
62.571094744970.375102847483-0.2361825163492.04800420208-0.04501386883134.336054067250.149217730522-0.242423585442-0.3101730298340.264839805320.02082884354550.08009135667750.209755196576-0.251370616206-0.09464609367310.145781400589-0.0265140036912-0.001863061576010.154594279920.05109214667910.194853991041-14.012158458930.2721325351.73442637585
72.954080896270.328282504350.4108134418334.36335584285-1.394634709193.47113544668-0.0198061902253-0.0233547558016-0.213931099454-0.06837402099730.04445500918530.1433454660820.0799678522759-0.0278877270734-0.0302729799060.0958660704695-0.0166247370604-0.02600555503980.121566861149-0.01924159059260.158922014245-14.539821084234.9773742131-5.38106140723
81.16014396505-0.1709314007082.118222112890.806364164601-0.7480258280124.50812464771-0.1425871574590.6279788424740.143534680161-0.192239412891-0.01502288412450.1157087871830.0917457102955-0.08070413261930.1434406364710.190654475955-0.0513515570013-0.03919547108670.3945381587030.01646911801070.2887411534-20.939295573142.6304974708-19.8392892409
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 145 )123 - 145122 - 144
44chain 'A' and (resid 146 through 161 )146 - 161145 - 160
55chain 'A' and (resid 162 through 185 )162 - 185161 - 177
66chain 'A' and (resid 186 through 206 )186 - 206178 - 198
77chain 'A' and (resid 207 through 228 )207 - 228199 - 220
88chain 'A' and (resid 229 through 252 )229 - 252221 - 242

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