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- PDB-6p9t: E.coli LpxA in complex with UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc... -

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Basic information

Entry
Database: PDB / ID: 6p9t
TitleE.coli LpxA in complex with UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc and Compound 8
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE/INHIBITOR / Acyltransferase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat ...Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-O5D / PHOSPHATE ION / Chem-U20 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMa, X. / Shia, S. / Ornelas, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis.
Authors: Han, W. / Ma, X. / Balibar, C.J. / Baxter Rath, C.M. / Benton, B. / Bermingham, A. / Casey, F. / Chie-Leon, B. / Cho, M.K. / Frank, A.O. / Frommlet, A. / Ho, C.M. / Lee, P.S. / Li, M. / ...Authors: Han, W. / Ma, X. / Balibar, C.J. / Baxter Rath, C.M. / Benton, B. / Bermingham, A. / Casey, F. / Chie-Leon, B. / Cho, M.K. / Frank, A.O. / Frommlet, A. / Ho, C.M. / Lee, P.S. / Li, M. / Lingel, A. / Ma, S. / Merritt, H. / Ornelas, E. / De Pascale, G. / Prathapam, R. / Prosen, K.R. / Rasper, D. / Ruzin, A. / Sawyer, W.S. / Shaul, J. / Shen, X. / Shia, S. / Steffek, M. / Subramanian, S. / Vo, J. / Wang, F. / Wartchow, C. / Uehara, T.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Refinement description
Category: citation / pdbx_refine_tls / pdbx_refine_tls_group
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6468
Polymers28,9461
Non-polymers1,7007
Water4,161231
1
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,93824
Polymers86,8383
Non-polymers5,10021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area15520 Å2
ΔGint-93 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.793, 95.793, 95.793
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-576-

HOH

31A-631-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / UDP-N-acetylglucosamine acyltransferase


Mass: 28945.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxA, EC958_0327 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W9AB79, UniProt: P0A722*PLUS, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-U20 / uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetyl-D-glucosamine / (2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydrox ytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-4-yl (3R)-3-hydroxytetradecanoate


Mass: 833.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H53N3O19P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-O5D / [3-(5-amino-4-methylpyridin-2-yl)-1H-pyrazol-5-yl]{(3R)-3-[(2-chloro-6-methoxyphenyl)methyl]morpholin-4-yl}methanone


Mass: 441.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.56 % / Mosaicity: 0.23 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Na/K phosphate, 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→67.74 Å / Num. obs: 29835 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.037 / Rrim(I) all: 0.108 / Net I/σ(I): 11.8 / Num. measured all: 239203
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.786.11.7511058917290.4550.7711.9160.8100
8.92-67.7412.50.0432922630.9990.0110.04247.499.4

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Processing

Software
NameVersionClassification
SCALA0.7.2data scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LXA

1lxa


Resolution: 1.75→47.896 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.07
RfactorNum. reflection% reflection
Rfree0.185 1418 4.76 %
Rwork0.1656 --
obs0.1665 29801 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.57 Å2 / Biso mean: 26.8171 Å2 / Biso min: 13.07 Å2
Refinement stepCycle: final / Resolution: 1.75→47.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 126 231 2341
Biso mean--32.63 40.17 -
Num. residues----263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7501-1.81270.29261440.270528112955
1.8127-1.88520.2381030.244428492952
1.8852-1.9710.2641630.188627672930
1.971-2.07490.19711660.161427922958
2.0749-2.2050.16781390.155828202959
2.205-2.37520.18021400.148328272967
2.3752-2.61420.17241330.152328402973
2.6142-2.99240.18381620.158628383000
2.9924-3.76990.17781210.157428752996
3.7699-47.91440.16321470.161729643111
Refinement TLS params.Method: refined / Origin x: 26.921 Å / Origin y: -3.381 Å / Origin z: -4.202 Å
111213212223313233
T0.1702 Å2-0.0155 Å20.014 Å2-0.1846 Å2-0.0019 Å2--0.1607 Å2
L0.411 °20.0332 °20.0608 °2-0.2699 °20.0801 °2--0.4496 °2
S-0.0036 Å °-0.0215 Å °0.0005 Å °0.0001 Å °0.0006 Å °0.029 Å °0.0183 Å °-0.1071 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:263 OR RESID 301:307 OR RESID 401:631 ) )A1 - 263
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:263 OR RESID 301:307 OR RESID 401:631 ) )A301 - 307
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:263 OR RESID 301:307 OR RESID 401:631 ) )A401 - 631

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