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- PDB-3p3e: Crystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 complex -

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Basic information

Entry
Database: PDB / ID: 3p3e
TitleCrystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LIPID A BIOSYNTHESIS / LIPID A SYNTHESIS / LPXC / baab sandwich / Deacetylation / ANTIBIOTIC / Acyl UDP-GlcNac / HYDROXAMATE / LPC-009
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-3P3 / NITRATE ION / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å
AuthorsLee, C.-J. / Zhou, P.
CitationJournal: Chem.Biol. / Year: 2011
Title: Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design.
Authors: Lee, C.J. / Liang, X. / Chen, X. / Zeng, D. / Joo, S.H. / Chung, H.S. / Barb, A.W. / Swanson, S.M. / Nicholas, R.A. / Li, Y. / Toone, E.J. / Raetz, C.R. / Zhou, P.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _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)35,21330
Polymers33,1471
Non-polymers2,06629
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.637, 73.608, 88.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Protein envA


Mass: 33146.617 Da / Num. of mol.: 1 / Fragment: UNP residues 1-299 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: envA, lpxC, PA4406 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P47205, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 442 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3P3 / N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide


Mass: 362.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N2O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate trihydrate pH 5.0, and 2.7 M ammonium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.0001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 88611 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.28-1.34.10.45694.9
1.3-1.335.10.439100
1.33-1.355.50.391100
1.35-1.385.80.355100
1.38-1.4160.324100
1.41-1.4460.276100
1.44-1.4860.24100
1.48-1.526.10.211100
1.52-1.566.10.181100
1.56-1.616.10.161100
1.61-1.676.10.147100
1.67-1.746.10.136100
1.74-1.826.10.126100
1.82-1.916.10.119100
1.91-2.036.10.114100
2.03-2.196.20.118100
2.19-2.416.20.126100
2.41-2.766.20.111100
2.76-3.476.10.104100
3.47-505.70.10298.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 26.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.1 Å
Translation2.5 Å26.1 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→22.99 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / σ(F): 0.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 4429 5.02 %
Rwork0.182 --
obs0.182 88305 99.5 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.09 Å2 / ksol: 0.47 e/Å3
Displacement parametersBiso mean: 21.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.2614 Å2-0 Å2-0 Å2
2---0.0819 Å2-0 Å2
3----0.1795 Å2
Refinement stepCycle: LAST / Resolution: 1.28→22.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 130 413 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092593
X-RAY DIFFRACTIONf_angle_d0.8573496
X-RAY DIFFRACTIONf_dihedral_angle_d11.988947
X-RAY DIFFRACTIONf_chiral_restr0.051383
X-RAY DIFFRACTIONf_plane_restr0.004473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.32680.25714070.25078143X-RAY DIFFRACTION98
1.3268-1.37990.23774220.22348340X-RAY DIFFRACTION100
1.3799-1.44270.22614470.20388305X-RAY DIFFRACTION100
1.4427-1.51870.20814320.19328327X-RAY DIFFRACTION100
1.5187-1.61390.20194140.18168375X-RAY DIFFRACTION100
1.6139-1.73840.19024560.18358363X-RAY DIFFRACTION100
1.7384-1.91330.18814790.17668346X-RAY DIFFRACTION100
1.9133-2.190.17944550.16698417X-RAY DIFFRACTION100
2.19-2.75840.19594480.1798528X-RAY DIFFRACTION100
2.7584-22.99150.1854690.1788732X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.4203 Å / Origin y: 3.9916 Å / Origin z: -7.8744 Å
111213212223313233
T0.0682 Å20.0063 Å2-0.0004 Å2-0.0806 Å2-0.0008 Å2--0.0819 Å2
L0.4192 °2-0.0545 °20.2016 °2-0.5059 °20.2002 °2--0.6718 °2
S0.0121 Å °0.0227 Å °-0.0067 Å °-0.0041 Å °0.029 Å °0.0095 Å °0.0303 Å °0.0317 Å °-0.036 Å °
Refinement TLS groupSelection details: CHAIN A AND RESID ALL

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