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- PDB-4isa: Crystal Structure of the Escherichia coli LpxC/BB-78485 complex -

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Basic information

Entry
Database: PDB / ID: 4isa
TitleCrystal Structure of the Escherichia coli LpxC/BB-78485 complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / LIPID A SYNTHESIS / LPXC / BAAB SANDWICH / DEACETYLATION / ANTIBIOTIC / ACYL UDP-GLCNAC / HYDROXAMATE / BB-78485 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / FORMIC ACID / Chem-GVR / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, C.-J. / Zhou, P.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structural Basis of the Promiscuous Inhibitor Susceptibility of Escherichia coli LpxC.
Authors: Lee, C.J. / Liang, X. / Gopalaswamy, R. / Najeeb, J. / Ark, E.D. / Toone, E.J. / Zhou, P.
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,39522
Polymers33,5541
Non-polymers1,84121
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.788, 106.788, 52.474
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase


Mass: 33554.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: IHE3034 / ExPEC / Gene: lpxC, ECOK1_0097 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D5CV28, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GVR / (2R)-N-hydroxy-3-naphthalen-2-yl-2-[(naphthalen-2-ylsulfonyl)amino]propanamide


Mass: 420.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N2O4S
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.57 Å3/Da / Density % sol: 52.22 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2010
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31675 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.835.10.51199.8
1.83-1.865.20.421100
1.86-1.95.10.354199.9
1.9-1.945.20.3111100
1.94-1.985.10.241199.9
1.98-2.035.20.2071100
2.03-2.085.30.1771100
2.08-2.135.30.1591100
2.13-2.25.40.139199.9
2.2-2.275.50.131100
2.27-2.355.50.112199.9
2.35-2.445.60.0981100
2.44-2.555.70.089199.9
2.55-2.695.60.077199.8
2.69-2.865.60.065199.7
2.86-3.085.70.055199.6
3.08-3.395.70.049199.7
3.39-3.885.70.046198.9
3.88-4.885.80.045198.5
4.88-505.70.051195.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.984 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 1577 5.06 %
Rwork0.1832 --
obs0.1846 31167 98 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.037 Å2 / ksol: 0.432 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1168 Å20 Å20 Å2
2---4.1168 Å20 Å2
3---8.2336 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 120 310 2787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082513
X-RAY DIFFRACTIONf_angle_d1.3453378
X-RAY DIFFRACTIONf_dihedral_angle_d12.817904
X-RAY DIFFRACTIONf_chiral_restr0.201370
X-RAY DIFFRACTIONf_plane_restr0.005434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85770.34381410.26062668X-RAY DIFFRACTION98
1.8577-1.92410.24191440.22652714X-RAY DIFFRACTION99
1.9241-2.0010.25181380.19972686X-RAY DIFFRACTION99
2.001-2.0920.2571360.18832728X-RAY DIFFRACTION99
2.092-2.20220.24431350.19122706X-RAY DIFFRACTION99
2.2022-2.340.23041390.1832696X-RAY DIFFRACTION99
2.34-2.52040.20681620.19052678X-RAY DIFFRACTION99
2.5204-2.77360.23551390.19622707X-RAY DIFFRACTION98
2.7736-3.17370.24281640.19742663X-RAY DIFFRACTION98
3.1737-3.9940.19121370.16612669X-RAY DIFFRACTION96
3.994-20.98490.1581420.16372675X-RAY DIFFRACTION95
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)
12.15460.5207-0.01192.81-0.51441.9268-0.03640.0190.03910.03420.05620.08640.04790.0195-0.01620.17840.01570.00940.1453-0.01090.1385-1.8574-45.9022-16.807
23.10521.5695-0.35633.08430.56712.43660.3494-0.56860.18550.7044-0.31960.32930.0425-0.16460.00750.32250.06340.06260.233-0.01030.2494-7.8143-39.7332.134
31.96080.4803-0.32061.3894-0.76862.4289-0.0361-0.30550.53170.3831-0.05080.3693-0.2453-0.04540.06420.31790.04030.04750.2625-0.06360.3566-5.1347-25.7275-6.5635
41.98930.3352-0.09772.46340.51841.437-0.07020.18840.248-0.00880.081-0.1949-0.10130.1224-0.01670.1941-0.0314-0.02650.20430.03190.247810.1163-24.728-19.8134
52.1140.696-0.41942.0948-0.24861.26320.0993-0.30460.09340.4309-0.09990.2497-0.0162-0.00380.00860.30050.00690.03720.227-0.04690.1864-3.207-37.5619-0.4997
67.2241-1.50212.50852.1289-0.51245.2167-0.40080.14331.4079-0.29550.45950.7682-0.5659-1.2877-0.04380.56180.08950.11170.57750.06170.742-22.9725-40.3165-2.3735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:118)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 119:148)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 149:191)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 192:233)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 234:285)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 286:300)

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