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- PDB-6ued: Apo Pseudomonas aeruginosa LpxD Structure -

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Basic information

Entry
Database: PDB / ID: 6ued
TitleApo Pseudomonas aeruginosa LpxD Structure
ComponentsUDP-3-O-acylglucosamine N-acyltransferase
KeywordsTRANSFERASE / LpxD / Apo / Trimer / Acyl Transferase
Function / homology
Function and homology information


UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase / N-acyltransferase activity / lipid A biosynthetic process
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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat ...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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
UDP-3-O-acylglucosamine N-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsChen, Y. / Kroeck, K. / Sacco, M.
CitationJournal: Sci Rep / Year: 2019
Title: Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography.
Authors: Kroeck, K.G. / Sacco, M.D. / Smith, E.W. / Zhang, X. / Shoun, D. / Akhtar, A. / Darch, S.E. / Cohen, F. / Andrews, L.D. / Knox, J.E. / Chen, Y.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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
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.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-acylglucosamine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3734
Polymers38,1641
Non-polymers2083
Water3,747208
1
A: UDP-3-O-acylglucosamine N-acyltransferase
hetero molecules

A: UDP-3-O-acylglucosamine N-acyltransferase
hetero molecules

A: UDP-3-O-acylglucosamine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,11812
Polymers114,4923
Non-polymers6259
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18170 Å2
ΔGint-138 kcal/mol
Surface area38040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.755, 104.755, 94.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-403-

MG

21A-563-

HOH

31A-670-

HOH

41A-690-

HOH

51A-693-

HOH

61A-707-

HOH

71A-708-

HOH

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Components

#1: Protein UDP-3-O-acylglucosamine N-acyltransferase


Mass: 38164.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lpxD, PA3646 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HXY6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3350 0.2M Magnesium Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 55962 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.02 / Rrim(I) all: 0.061 / Χ2: 0.946 / Net I/σ(I): 10.6 / Num. measured all: 604118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.55-1.585.927010.6170.5070.75298.1
1.58-1.617.528150.7490.4390.79999.8
1.61-1.649.128050.7740.4010.806100
1.64-1.6710.228200.810.3480.818100
1.67-1.7110.827710.8670.280.8521000.8710.916
1.71-1.751128620.9180.2220.891000.6960.731
1.75-1.7911.327590.9470.1860.9271000.5930.622
1.79-1.8411.328220.9710.1340.9561000.4260.447
1.84-1.8911.428060.9850.10.9691000.3220.337
1.89-1.9511.527990.9920.0721.0381000.2320.243
1.95-2.0211.627940.9950.0561.1081000.1810.189
2.02-2.111.628020.9950.0431.1011000.1380.144
2.1-2.211.628360.9970.0321.091000.1050.11
2.2-2.3211.627630.9970.0271.0421000.0880.092
2.32-2.4611.628030.9980.0231.0391000.0740.077
2.46-2.6511.728130.9980.0211.0981000.0690.072
2.65-2.9211.628230.9990.0171.0411000.0540.057
2.92-3.3411.627780.9990.0130.9221000.0430.045
3.34-4.2111.528190.9990.0110.7881000.0350.036
4.21-5011.327710.9990.0110.65198.70.0330.035

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.505
Highest resolutionLowest resolution
Rotation32.69 Å1.73 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→32.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.352 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 2778 5.1 %RANDOM
Rwork0.1757 ---
obs0.1766 51180 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.5 Å2 / Biso mean: 18.442 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.55→32.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 13 208 2642
Biso mean--27.83 28.35 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132551
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172392
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6243474
X-RAY DIFFRACTIONr_angle_other_deg1.4491.5715509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48421.171111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7661518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022997
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02533
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.286 139 -
Rwork0.265 2461 -
obs--62.94 %

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