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- PDB-7ss7: Crystal structure of Klebsiella LpxH in complex with JH-LPH-50 -

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Basic information

Entry
Database: PDB / ID: 7ss7
TitleCrystal structure of Klebsiella LpxH in complex with JH-LPH-50
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE/ANTIBIOTIC / LpxH / lipid A / LPS / antibiotic / Gram-negative bacteria / HYDROLASE-ANTIBIOTIC complex
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-BN8 / : / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsCho, J. / Cochrane, C.S. / 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: Chemmedchem / Year: 2023
Title: Development of LpxH Inhibitors Chelating the Active Site Dimanganese Metal Cluster of LpxH.
Authors: Kwak, S.H. / Skyler Cochrane, C. / Cho, J. / Dome, P.A. / Ennis, A.F. / Kim, J.H. / Zhou, P. / Hong, J.
History
DepositionNov 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,70210
Polymers29,6281
Non-polymers1,0749
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.530, 106.530, 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
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-607-

HOH

31A-640-

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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BN8 / 6-{[(4-{4-[3-chloro-5-(trifluoromethyl)phenyl]piperazine-1-sulfonyl}phenyl)carbamoyl]amino}-N-hydroxyhexanamide


Mass: 592.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29ClF3N5O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4 mg/mL of LpxH, 0.27 mM JH-LPH-50, 10 mM MES (pH 6.0), 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 0.625% DMSO, 0.05 M calcium chloride dihydrate, 0.05 M Tris pH 6.5, 6.5 % w/v PEG 2000 MME

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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 / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.73→46.32 Å / Num. obs: 36774 / % possible obs: 99.94 % / Redundancy: 11.6 % / Biso Wilson estimate: 21.65 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 21.98
Reflection shellResolution: 1.73→1.792 Å / Num. unique obs: 3624 / CC1/2: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PJ3

6pj3


Resolution: 1.73→46.32 Å / SU ML: 0.1834 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1931 1839 5 %
Rwork0.1681 34926 -
obs0.1693 36765 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.24 Å2
Refinement stepCycle: LAST / Resolution: 1.73→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 65 242 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742125
X-RAY DIFFRACTIONf_angle_d0.88132896
X-RAY DIFFRACTIONf_chiral_restr0.0623300
X-RAY DIFFRACTIONf_plane_restr0.0077384
X-RAY DIFFRACTIONf_dihedral_angle_d17.2964304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.780.27481400.27382664X-RAY DIFFRACTION99.86
1.78-1.830.25041390.21092638X-RAY DIFFRACTION99.86
1.83-1.890.22971400.17552663X-RAY DIFFRACTION99.96
1.89-1.960.23811410.18512663X-RAY DIFFRACTION99.93
1.96-2.030.2061390.17812654X-RAY DIFFRACTION100
2.03-2.130.20951420.16022688X-RAY DIFFRACTION99.96
2.13-2.240.19421400.15672664X-RAY DIFFRACTION100
2.24-2.380.17721400.15672667X-RAY DIFFRACTION99.96
2.38-2.560.211420.16582697X-RAY DIFFRACTION100
2.56-2.820.18431420.16292694X-RAY DIFFRACTION100
2.82-3.230.18041420.17152696X-RAY DIFFRACTION100
3.23-4.070.16921430.14952722X-RAY DIFFRACTION99.9
4.07-46.320.19011490.17352816X-RAY DIFFRACTION99.97
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)
12.9298588123-1.061301854240.5567127292152.98547370443-1.24727971512.672715773060.06716489470970.200360750723-0.201393877633-0.370309329552-0.09411161841540.05264986687830.222809250245-0.0497904539219-0.0003729858627990.1748561030880.0212023265683-0.002128528801390.138597851604-0.03859077871530.149131329869-36.6472433652-31.08413704-1.17573672388
21.68060370303-0.7415463952220.3761774068722.31875709859-0.3194544861671.182298887240.0211670767413-0.008331956671780.0135245780769-0.0938140115064-0.02054178368670.160780487561-0.0437813249656-0.0860827295077-0.004549266395990.1283268590730.011480673942-0.001552260178240.130782082548-0.01355009241410.159160694873-42.6069306454-23.83850525963.96605123741
32.72053578021-0.577177004954-0.1642932770973.18653734499-0.6166578546321.77216286727-0.0296958276182-0.2369715053810.06297939157820.2097024358310.0153356748063-0.140339043714-0.03307206753990.1280424122040.0243811610850.1554604679680.01731879360540.006818776348320.147970643022-0.02450819141850.0943516178891-32.7958901693-26.135354389112.8753818484
42.78896676821-3.343798668120.1732704247674.065151476660.4772073071592.60909291242-0.43425176105-0.7277607694520.5474660941290.5091915427950.390892826481-0.496106376423-0.0729691702040.1234142275250.05576345448090.2768841136550.0519434878877-0.06606462122760.189391563637-0.06733046768880.266615992879-37.2267282793-7.3858043272912.871269488
59.343134550956.6356389518-4.468051024978.48096988548-3.180656644792.26129156246-0.3352934820540.4242291801240.0377976059942-0.8100567703050.08237848800460.185996058383-0.0335781861008-0.09939857733380.1433428558440.2700403410590.0339566197926-0.04090491608860.165123430287-0.01684856780760.187864020992-44.5199122746-4.68583831547-0.257342102971
64.11279909907-3.36935158898-0.5783216113875.08850546145-0.3820422443310.342941368358-0.037434790023-0.1384289078550.5118890516120.0797483421963-0.210878749954-0.530778594746-0.2849618927240.1895133091710.1609633684420.237914587889-0.0281973743271-0.05465659120080.239264635347-0.06619566559510.295870765772-18.6722583963-19.429561256613.1152103105
74.32758100501-0.3919526660831.464456750022.079908106040.6613359643284.526982778170.0435714837601-0.02403643260910.0598670030080.08043269664380.0282205859387-0.2414703332670.03371903172630.180911240947-0.07127227294780.1028882017530.01971655913980.003925857752190.115313006759-0.01443991126940.160426212078-21.1423730196-29.08239912787.06694219535
81.26698843557-1.54665765671-2.03347112422.077697242872.805520295663.602258723710.06268896613330.120203275067-0.165667376928-0.265896739195-0.257836045120.137135002048-0.352867969252-0.7914837713820.1759302542080.160849476722-0.00304839866697-0.007509858688550.192578506475-0.008048133976930.254693119752-27.8530628827-38.7336068423-7.42131561592
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 143 )123 - 143122 - 142
55chain 'A' and (resid 144 through 156 )144 - 156143 - 155
66chain 'A' and (resid 157 through 185 )157 - 185156 - 172
77chain 'A' and (resid 186 through 228 )186 - 228173 - 215
88chain 'A' and (resid 229 through 249 )229 - 249216 - 236

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