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- PDB-6e54: Crystal structure of LpxC from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 6.0E+54
TitleCrystal structure of LpxC from Pseudomonas aeruginosa in complex with ligand PT802
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
Keywordshydrolase/hydrolase inhibitor / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / LpxC / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / : / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HUM / Chem-JCG / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of LpxC from Pseudomonas aeruginosa in complex with ligand PT802
Authors: Delker, S.L. / Mayclin, S.J. / Phan, J.N. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7568
Polymers33,5621
Non-polymers1,1947
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.640, 47.740, 48.350
Angle α, β, γ (deg.)111.68, 107.87, 99.27
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33562.125 Da / Num. of mol.: 1 / Fragment: PsaeA.00166.a.DG15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lpxC, envA, PA4406 / Plasmid: PsaeA.00166.a.DG15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase

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Non-polymers , 6 types, 397 molecules

#2: Chemical ChemComp-HUM / (2S)-4-{4-[4-(benzyloxy)-2-fluorophenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide


Mass: 488.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25FN2O6S
#3: Chemical ChemComp-JCG / (2R)-4-{4-[4-(benzyloxy)-2-fluorophenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide


Mass: 488.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25FN2O6S
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: tray298106 C1: 100 mM Tris-HCl, pH 8.5, 100 mM MgCl, 25% (w/v) Peg 400, 20% (w/v) PEG 3350, 1mM BSI108452 (PT802) : Cryo = direct : PsaeA.00166.a.DG15.PD00471 at 5 mg/ml, puck zot8-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2018 / Details: mirrors
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→39.582 Å / Num. obs: 31220 / % possible obs: 96.4 % / Redundancy: 3.926 % / Biso Wilson estimate: 10.37 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.108 / Χ2: 1.004 / Net I/σ(I): 10.81 / Num. measured all: 122571
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.693.5460.4832.5121770.7710.57289.4
1.69-1.743.8970.4193.1421980.8540.48696.1
1.74-1.793.9780.3413.9221770.9070.39495
1.79-1.843.980.2974.5721120.9220.34496.5
1.84-1.913.9830.2245.920440.9550.25895.9
1.91-1.973.9820.1917.0419870.9620.22196.1
1.97-2.053.9750.1528.619250.9760.17697.2
2.05-2.133.9730.1379.5318630.9790.15896.6
2.13-2.223.9650.1210.5617850.9850.13996.5
2.22-2.333.9660.10911.6916950.9860.12697.5
2.33-2.463.9710.09612.8816450.9890.11297.5
2.46-2.613.960.0913.5515330.9910.10497.2
2.61-2.793.950.08215.114670.9910.09497.5
2.79-3.013.9460.0716.6613740.9940.08197.8
3.01-3.33.9260.05719.2712290.9960.06698.2
3.3-3.693.9050.0522.1911410.9960.05898.6
3.69-4.263.9140.04524.2310160.9970.05299
4.26-5.223.9340.04325.68370.9970.04998
5.22-7.383.9140.04424.696530.9970.05198
7.38-39.5823.8230.03726.953620.9980.04397.8

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Processing

Software
NameVersionClassification
PHENIX(1.14rc2_3191: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
XDSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UPG

5upg


Resolution: 1.65→39.582 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 17.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1847 1953 6.26 %
Rwork0.1492 --
obs0.1514 31216 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→39.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 73 390 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062579
X-RAY DIFFRACTIONf_angle_d0.9413528
X-RAY DIFFRACTIONf_dihedral_angle_d18.6781574
X-RAY DIFFRACTIONf_chiral_restr0.055402
X-RAY DIFFRACTIONf_plane_restr0.005455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.23191230.21671967X-RAY DIFFRACTION89
1.6913-1.7370.21651550.19432037X-RAY DIFFRACTION96
1.737-1.78810.25281490.18682042X-RAY DIFFRACTION96
1.7881-1.84580.22891350.18112093X-RAY DIFFRACTION97
1.8458-1.91180.21391390.16582068X-RAY DIFFRACTION96
1.9118-1.98830.22931220.15382123X-RAY DIFFRACTION96
1.9883-2.07880.19611420.1492090X-RAY DIFFRACTION97
2.0788-2.18840.17561540.15032100X-RAY DIFFRACTION97
2.1884-2.32550.19021350.14692073X-RAY DIFFRACTION97
2.3255-2.5050.20531610.14772113X-RAY DIFFRACTION98
2.505-2.75710.1781410.14942111X-RAY DIFFRACTION98
2.7571-3.15590.18241310.15252148X-RAY DIFFRACTION99
3.1559-3.97550.14011240.12492162X-RAY DIFFRACTION99
3.9755-39.59360.14621420.12452136X-RAY DIFFRACTION99
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)
10.3086-0.010.06521.13450.2010.66090.01570.05050.0047-0.0682-0.06070.0592-0.0512-0.08460.02010.05970.01490.00260.06650.01320.0739-5.46686.3439-12.0588
21.03560.2564-0.3211.18980.07690.83560.037-0.00670.0471-0.0113-0.0228-0.0593-0.06620.0432-0.0030.06550.0149-0.00280.05570.02030.05-1.80076.133-5.1148
31.9674-0.43011.00011.18580.21882.23770.0830.0069-0.11860.06270.0587-0.07640.15670.1657-0.1550.0266-0.01640.03090.03240.01980.06176.7769-9.4114-1.6684
40.9864-1.8543-2.56623.50744.77416.782-0.0596-0.1104-0.05860.32350.0249-0.02590.40470.02560.06170.0795-0.0198-0.0040.10790.01310.0833-0.6881-5.874115.4812
50.99870.0961-0.2721.35760.46741.71220.0482-0.05710.00010.1253-0.09030.1020.0045-0.08480.04330.05050.0051-0.00830.08140.0180.0571-6.64183.178510.2036
61.33281.0170.57541.21370.82361.0709-0.00120.0293-0.05010.0110.0216-0.03790.06130.0274-0.02310.05540.0236-0.00120.05110.02520.07495.2209-10.2207-3.177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 170 )
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 299 )

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