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- PDB-6p87: E.coli LpxD in complex with compound 5 -

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Basic information

Entry
Database: PDB / ID: 6p87
TitleE.coli LpxD in complex with compound 5
ComponentsUDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
KeywordsTRANSFERASE/INHIBITOR / lps synthesis / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase activity / UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase / N-acyltransferase activity / lipid A biosynthetic process / response to antibiotic / identical protein binding / cytosol / cytoplasm
Similarity search - Function
UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-O3V / Chem-O4P / UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase / UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMa, X. / Shia, S.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structural and Biological Basis of Small Molecule Inhibition ofEscherichia coliLpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis.
Authors: Ma, X. / Prathapam, R. / Wartchow, C. / Chie-Leon, B. / Ho, C.M. / De Vicente, J. / Han, W. / Li, M. / Lu, Y. / Ramurthy, S. / Shia, S. / Steffek, M. / Uehara, T.
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
B: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
C: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5388
Polymers108,3043
Non-polymers1,2345
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18750 Å2
ΔGint-164 kcal/mol
Surface area38100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.213, 97.213, 216.185
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-780-

HOH

21A-781-

HOH

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Components

#1: Protein UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase / UDP-3-O-(3-OHC14)-GlcN N-acyltransferase / UDP-3-O-(3-hydroxytetradecanoyl)glucosamine N-acyltransferase


Mass: 36101.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: lpxD, lpxD_1, lpxD_2, A8C65_17800, A9R57_04450, AC789_1c01770, ACN002_0184, ACN77_17005, ACN81_28485, ACU57_18525, ACU90_26495, AM270_18210, AML07_22885, AML35_22825, APZ14_11060, AUQ13_07450, ...Gene: lpxD, lpxD_1, lpxD_2, A8C65_17800, A9R57_04450, AC789_1c01770, ACN002_0184, ACN77_17005, ACN81_28485, ACU57_18525, ACU90_26495, AM270_18210, AML07_22885, AML35_22825, APZ14_11060, AUQ13_07450, AUS26_23195, AW059_09890, AW106_08805, B1K96_12940, B7C53_01310, BANRA_00558, BANRA_00653, BANRA_02262, BANRA_03350, BET08_19125, BHF46_07835, BHS81_00700, BHS87_00855, BIZ41_19025, BJJ90_21310, BK292_13720, BK400_03560, BMT53_09465, BN17_46021, BTQ06_06540, BUE81_01655, BVL39_02135, BW690_02415, BZL31_14885, C2U48_09555, C4J69_03380, C5N07_08630, C5P01_08975, C5P43_07335, C6669_04195, C6986_01145, C7235_20180, C7B06_05915, C7B07_04225, CA593_02815, CG691_14440, CG692_09445, CG705_12975, CG706_12690, COD30_14715, COD46_06685, CR538_20590, CR539_04985, CRM83_15040, CXB56_23080, D0X26_09365, D2184_08545, D2185_20180, D2F89_01460, D3821_06260, D3O91_03240, D3Y67_16455, D9D20_18680, D9D55_03030, D9D69_06830, D9E22_13300, D9E35_14480, D9G42_07535, D9H66_18155, D9H68_13825, D9I18_15010, D9I87_01590, D9I97_03755, D9J11_16875, D9J44_14030, DIV22_06320, DL545_20340, DMZ31_06810, DNQ41_04690, DNQ45_10065, DQF57_05615, DQO13_06200, DS732_05825, DTL43_05870, EAI42_08350, EAI46_03595, EAI52_11055, EC1094V2_3672, EC3234A_2c01610, EC3426_00931, EC382_03005, ECTO6_03883, ED287_04550, ED600_04595, EEP23_00115, EFV01_09910, EFV02_20465, EFV04_15215, EFV08_17150, EFV11_08135, EFV12_18845, EFV15_17225, EFV17_09875, EIA13_13600, EL75_3585, EL79_3695, EL80_3642, ERS085374_03841, ERS150873_01122, ERS150876_00054, FORC28_5013, HW43_04650, JD73_13090, NCTC10429_04183, NCTC10865_05054, NCTC11022_04906, NCTC11126_03647, NCTC13462_02218, NCTC8500_04533, NCTC8960_01551, NCTC9037_04178, NCTC9045_04699, NCTC9055_00956, NCTC9058_02808, NCTC9062_04225, NCTC9706_01326, NCTC9969_04255, PU06_22990, RG28_03860, RK56_027945, RX35_04913, SAMEA3472043_02537, SAMEA3472044_04146, SAMEA3472047_02509, SAMEA3472070_02384, SAMEA3472080_03763, SAMEA3472114_03609, SAMEA3484427_01386, SAMEA3484429_01095, SAMEA3752553_02884, SAMEA3752557_00885, SAMEA3752559_03701, SAMEA3753064_03381, SAMEA3753097_03916, SAMEA3753290_00404, SAMEA3753300_01852, SK85_00179, WQ89_09605, WR15_02380
Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0P6M7, UniProt: P21645*PLUS, UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-O4P / N-[(R)-(1H-indol-3-yl)(thiophen-2-yl)methyl]-2-(2-methoxyphenoxy)-N-methylacetamide


Mass: 406.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-O3V / 3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one


Mass: 389.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19N3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.49 % / Mosaicity: 0.2 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Mg formate, 20% PEG 3350

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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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2014
RadiationMonochromator: DOUBLE CRYSTAL Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→84.19 Å / Num. obs: 94046 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.037 / Rrim(I) all: 0.102 / Net I/σ(I): 14.3 / Num. measured all: 686750
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
1.9-1.9371.2383212446020.6280.5041.3391.6100
10.41-84.196.20.019428268810.0080.02155.799.6

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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: 3EH0

3eh0


Resolution: 1.9→84.189 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.5
RfactorNum. reflection% reflection
Rfree0.2069 4642 4.94 %
Rwork0.1798 --
obs0.1811 93926 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.01 Å2 / Biso mean: 31.9633 Å2 / Biso min: 17.15 Å2
Refinement stepCycle: final / Resolution: 1.9→84.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7448 0 87 985 8520
Biso mean--32.93 40.97 -
Num. residues----1011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.28921430.283929163059100
1.9216-1.94420.26621560.265129843140100
1.9442-1.96790.29141610.255128903051100
1.9679-1.99280.26781560.24529503106100
1.9928-2.01910.28241680.230529363104100
2.0191-2.04670.25891270.231929543081100
2.0467-2.0760.2341480.222129933141100
2.076-2.10690.281570.213629283085100
2.1069-2.13990.24791400.212229403080100
2.1399-2.1750.22371610.196729263087100
2.175-2.21250.22171800.194529453125100
2.2125-2.25270.23111390.189129623101100
2.2527-2.2960.19651330.187429543087100
2.296-2.34290.1861410.1929953136100
2.3429-2.39380.22851540.181529373091100
2.3938-2.44950.23511710.184229463117100
2.4495-2.51080.20241650.189729313096100
2.5108-2.57870.23531800.188429483128100
2.5787-2.65460.21311570.186329443101100
2.6546-2.74030.24711300.187330043134100
2.7403-2.83820.2161660.185329573123100
2.8382-2.95180.21351720.178329983170100
2.9518-3.08620.2161500.178829613111100
3.0862-3.24890.19611310.174630413172100
3.2489-3.45250.19921600.173229773137100
3.4525-3.7190.18851730.164530023175100
3.719-4.09330.17921440.150130433187100
4.0933-4.68560.16571550.134430313186100
4.6856-5.90310.18771720.165230543226100
5.9031-84.27170.17551520.17883237338999
Refinement TLS params.Method: refined / Origin x: -21.1011 Å / Origin y: 41.7281 Å / Origin z: 15.8258 Å
111213212223313233
T0.2007 Å2-0.0228 Å20.0085 Å2-0.1757 Å2-0.0039 Å2--0.1858 Å2
L0.2752 °20.1048 °20.065 °2-0.2573 °20.0183 °2--0.2706 °2
S0.0108 Å °-0.0186 Å °-0.0085 Å °0.0085 Å °-0.0397 Å °0.0049 Å °-0.0088 Å °-0.0127 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 337
2X-RAY DIFFRACTION1allA401 - 501
3X-RAY DIFFRACTION1allB2 - 340
4X-RAY DIFFRACTION1allB501
5X-RAY DIFFRACTION1allC2 - 338
6X-RAY DIFFRACTION1allC501
7X-RAY DIFFRACTION1allS1 - 985

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