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- PDB-5n8c: Crystal structure of Pseudomonas aeruginosa LpxC complexed with i... -

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Basic information

Entry
Database: PDB / ID: 5n8c
TitleCrystal structure of Pseudomonas aeruginosa LpxC complexed with inhibitor
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / inhibitor / LpxC / hyroxamate / antibacterial
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-8Q8 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCross, J.B. / Ryan, M.D. / Zhang, J. / Cheng, R.K. / Wood, M. / Andersen, O.A. / Brooks, M. / Kwong, J. / Barker, J.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Structure-based discovery of LpxC inhibitors.
Authors: Zhang, J. / Chan, A. / Lippa, B. / Cross, J.B. / Liu, C. / Yin, N. / Romero, J.A. / Lawrence, J. / Heney, R. / Herradura, P. / Goss, J. / Clark, C. / Abel, C. / Zhang, Y. / Poutsiaka, K.M. / ...Authors: Zhang, J. / Chan, A. / Lippa, B. / Cross, J.B. / Liu, C. / Yin, N. / Romero, J.A. / Lawrence, J. / Heney, R. / Herradura, P. / Goss, J. / Clark, C. / Abel, C. / Zhang, Y. / Poutsiaka, K.M. / Epie, F. / Conrad, M. / Mahamoon, A. / Nguyen, K. / Chavan, A. / Clark, E. / Li, T.C. / Cheng, R.K. / Wood, M. / Andersen, O.A. / Brooks, M. / Kwong, J. / Barker, J. / Parr, I.B. / Gu, Y. / Ryan, M.D. / Coleman, S. / Metcalf, C.A.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr1_symmetry / _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 / _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
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,37210
Polymers67,0922
Non-polymers1,2808
Water8,863492
1
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1865
Polymers33,5461
Non-polymers6404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1865
Polymers33,5461
Non-polymers6404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.440, 95.310, 89.720
Angle α, β, γ (deg.)90.000, 96.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 33546.062 Da / Num. of mol.: 2 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lpxC, envA, PA4406 / Plasmid: pBADsmt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta 2
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8Q8 / (2~{S})-3-azanyl-2-[[(1~{R})-5-[2-[4-[[2-(hydroxymethyl)imidazol-1-yl]methyl]phenyl]ethynyl]-2,3-dihydro-1~{H}-inden-1-yl]amino]-3-methyl-~{N}-oxidanyl-butanamide


Mass: 473.567 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31N5O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG3350, 0.1 M Imidazole, 0.1M CaCl2, 1mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2010 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→44.59 Å / Num. obs: 46511 / % possible obs: 99.6 % / Redundancy: 4.3 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.126 / Rsym value: 0.11 / Net I/av σ(I): 5.5 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.9-24.30.4351.70.2350.4960.43599.6
2-2.124.30.2762.70.1480.3140.27699.7
2.12-2.274.30.2163.40.1170.2460.21699.7
2.27-2.454.30.1674.40.090.190.16799.6
2.45-2.694.30.1315.50.0710.1490.13199.7
2.69-34.30.0957.30.0510.1080.09599.6
3-3.474.20.0768.50.0410.0870.07699.8
3.47-4.254.10.078.70.0390.0810.0799.3
4.25-6.0140.0628.60.0340.0710.06299.4
6.01-44.594.30.0511.10.0270.0570.0599.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.59 Å
Translation2.5 Å44.59 Å

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VES

2ves


Resolution: 1.9→44.59 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.253 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1421 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.138
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2395 5.2 %RANDOM
Rwork0.1492 ---
obs0.1519 44092 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.13 Å2 / Biso mean: 19.655 Å2 / Biso min: 3.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.31 Å2
2--1.4 Å20 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.9→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 76 501 5255
Biso mean--16.52 30.71 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195029
X-RAY DIFFRACTIONr_bond_other_d0.0020.024819
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9816845
X-RAY DIFFRACTIONr_angle_other_deg1.067311164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41123.605233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49915893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7591544
X-RAY DIFFRACTIONr_chiral_restr0.1230.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025643
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021073
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 183 -
Rwork0.216 3257 -
all-3440 -
obs--99.42 %

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