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- PDB-7ss6: Structure of Klebsiella LpxH in complex with JH-LPH-45 -

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Basic information

Entry
Database: PDB / ID: 7ss6
TitleStructure of Klebsiella LpxH in complex with JH-LPH-45
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE/ANTIBIOTIC / LpxH / lipid A / 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-BKB / : / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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)30,5908
Polymers29,6281
Non-polymers9627
Water2,738152
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)105.820, 105.820, 53.620
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BKB / 5-{4-[3-chloro-5-(trifluoromethyl)phenyl]piperazine-1-sulfonyl}-N-[5-(hydroxyamino)-5-oxopentyl]-2,3-dihydro-1H-indole-1-carboxamide


Mass: 604.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29ClF3N5O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4 mg/mL protein, 0.27 mM JH-LPH-45, 10 mM MES (pH 6.0), 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 0.625% DMSO, 0.025 M magnesium acetate tetrahydrate, 0.025 M sodium acetate pH 5.4, 12% v/v PEG400

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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: 1.74→46.28 Å / Num. obs: 35718 / % possible obs: 99.95 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 24.31
Reflection shellResolution: 1.74→1.8 Å / Num. unique obs: 3542 / CC1/2: 0.934

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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: 1.74→46.28 Å / SU ML: 0.1486 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.5452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1947 1788 5.01 %
Rwork0.1667 33929 -
obs0.1681 35717 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.95 Å2
Refinement stepCycle: LAST / Resolution: 1.74→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 58 152 2155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722144
X-RAY DIFFRACTIONf_angle_d0.93722925
X-RAY DIFFRACTIONf_chiral_restr0.0633304
X-RAY DIFFRACTIONf_plane_restr0.0078385
X-RAY DIFFRACTIONf_dihedral_angle_d11.9328304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.29711360.25892571X-RAY DIFFRACTION99.71
1.79-1.840.20941360.19932579X-RAY DIFFRACTION99.93
1.84-1.90.25281360.19452581X-RAY DIFFRACTION99.96
1.9-1.970.21881360.18852593X-RAY DIFFRACTION99.96
1.97-2.050.21711370.1782600X-RAY DIFFRACTION100
2.05-2.140.17981360.1522586X-RAY DIFFRACTION99.96
2.14-2.250.19461370.15462594X-RAY DIFFRACTION100
2.25-2.390.18831370.15922602X-RAY DIFFRACTION99.96
2.39-2.580.18481370.1722598X-RAY DIFFRACTION100
2.58-2.840.20791380.16522620X-RAY DIFFRACTION100
2.84-3.250.19821370.16842609X-RAY DIFFRACTION100
3.25-4.090.17631400.14872664X-RAY DIFFRACTION99.93
4.09-46.280.1891450.17052732X-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)
11.10921731042-0.4595917516740.04343333763310.2358883582240.3928235085680.609035820945-0.009201513994660.002661556542910.0344001365625-0.0539812087287-0.0159645648429-0.01150774342790.002448705925920.0231926066239-1.73541594489E-50.2288616244020.008935389936950.02231254559960.1884482328350.01977437778010.21183820067239.905617536726.8486227131.65365273626
20.500214732479-0.2846978714510.4791231269320.3599552531690.1076556207490.65555662681-0.111818283543-0.243894690267-0.1757710397760.1906470662660.06357843009250.09380879514180.0498301116265-0.114589501496-3.46345248876E-50.257638335160.01386291566890.02945362442030.2683852977150.01967722248520.24123747261332.21805064625.543791965412.894945681
30.809270737827-0.009698847943280.445793960930.4113670961040.1154538668250.954931085567-0.594945102321-0.164019377013-0.4965857233490.4233905468270.3400235092080.4378579213820.201738538510.05812392122610.1842699003080.3914983112890.1044132053120.1144103983520.2345913285070.1198376664450.38960887900937.0956559237.2297294896112.0748689322
40.0183274595273-0.0242470025386-0.00748196967520.127559535285-0.09705500383720.144220217679-0.08337955662480.112037306052-0.172103395624-0.56688727261-0.2223346497010.1545485400270.2403148372110.0491077034835-0.005351668620880.4671340740930.0415098666673-0.006879864811320.25264523437-0.01561234015740.33026112941141.16986690425.32950635097-1.63105967095
50.892251642881-0.5420280465070.6732171844140.440871233027-0.1547768704240.620353809958-0.0460032045409-0.00594153102316-0.1950378448680.02980423490220.05678843664890.2871208959020.0436285568149-0.158941625175-0.001584460361930.2130188489920.0009471466836240.06569433676140.2381711678430.01196823188410.25214880101920.315476232525.83726635198.66448568079
60.0755215060288-0.2398353416280.04272998517080.237855304236-0.1181125087640.1035275571530.09516066694250.08279197769120.134716331869-0.0689950571848-0.138958011235-0.128025406954-0.118346568348-0.1354113824040.002885784560510.2936107387230.07055902801260.02629983401330.2666586307360.02606472479220.28784319841426.924003207639.2333361421-11.5504675264
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 85 )2 - 851 - 84
22chain 'A' and (resid 86 through 122 )86 - 12285 - 121
33chain 'A' and (resid 123 through 145 )123 - 145122 - 144
44chain 'A' and (resid 146 through 160 )146 - 160145 - 159
55chain 'A' and (resid 161 through 228 )161 - 228160 - 219
66chain 'A' and (resid 229 through 252 )229 - 252220 - 243

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