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- PDB-5drr: Crystal structure of the Pseudomonas aeruginosa LpxC/LPC-058 complex -

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Basic information

Entry
Database: PDB / ID: 5drr
TitleCrystal structure of the Pseudomonas aeruginosa LpxC/LPC-058 complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
Keywordshydrolase/hydrolase inhibitor / LpxC / Lipid A / Inhibitor / Gram-negative bacteria / 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 / membrane
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-5EN / NITRATE ION / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsLee, C.-J. / Najeeb, J. / Zhou, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI055588 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094475 United States
CitationJournal: Nat Commun / Year: 2016
Title: Drug design from the cryptic inhibitor envelope.
Authors: Lee, C.J. / Liang, X. / Wu, Q. / Najeeb, J. / Zhao, J. / Gopalaswamy, R. / Titecat, M. / Sebbane, F. / Lemaitre, N. / Toone, E.J. / Zhou, P.
History
DepositionSep 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,75921
Polymers33,1471
Non-polymers1,61220
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.830, 73.900, 88.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: lpxC, envA, 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5EN / 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3S)-4,4-difluoro-3-hydroxy-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]benzamide


Mass: 427.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19F2N3O4
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate, 2.4 - 2.6 M ammonium nitrate,
PH range: 4.8 - 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.59→28.319 Å / Num. all: 46207 / Num. obs: 46207 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 21.26 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.057 / Rsym value: 0.047 / Net I/av σ(I): 10.909 / Net I/σ(I): 14.9 / Num. measured all: 230581
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.59-1.684.80.4241.83085164210.2390.4242.795.3
1.68-1.784.70.2652.82896061280.150.2654.295.7
1.78-1.94.70.1684.42733658440.0940.1686.396.8
1.9-2.054.70.17.32641855790.0550.110.598.5
2.05-2.2550.0729.52604552110.0390.07215.299.9
2.25-2.515.30.05213.12508147530.0270.05219.2100
2.51-2.95.40.05111.62263041850.0250.05124.3100
2.9-3.565.40.04115.21962836120.020.04132.1100
3.56-5.035.40.02823.21524528270.0140.02837.8100
5.03-28.3195.10.02623838716470.0130.0263499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3E

3p3e


Resolution: 1.59→28.319 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 2321 5.04 %
Rwork0.1787 43718 -
obs0.1802 46039 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.93 Å2 / Biso mean: 26.5204 Å2 / Biso min: 13.46 Å2
Refinement stepCycle: final / Resolution: 1.59→28.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 101 261 2655
Biso mean--31.42 33.72 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042455
X-RAY DIFFRACTIONf_angle_d0.8023310
X-RAY DIFFRACTIONf_chiral_restr0.029371
X-RAY DIFFRACTIONf_plane_restr0.004443
X-RAY DIFFRACTIONf_dihedral_angle_d12.897900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.62250.27711290.26252461259095
1.6225-1.65770.27861290.23692441257094
1.6577-1.69630.22621220.22562491261395
1.6963-1.73870.2591450.22442454259995
1.7387-1.78570.28281260.23012482260895
1.7857-1.83830.26381220.22452521264396
1.8383-1.89760.27361430.22322516265997
1.8976-1.96540.28171180.20572542266098
1.9654-2.04410.21811380.18442584272299
2.0441-2.13710.19211310.177926122743100
2.1371-2.24970.22971360.20832582271898
2.2497-2.39060.23811620.1842601276399
2.3906-2.5750.21081410.177626052746100
2.575-2.83390.22411390.182226462785100
2.8339-3.24350.19381400.1826762816100
3.2435-4.08450.16891270.145227112838100
4.0845-28.3230.17871730.146327932966100
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)
11.0177-1.09091.26064.22670.77162.9778-0.072-0.0061-0.00920.05470.2327-0.01740.03880.1617-0.1490.0966-0.02570.00280.1630.02940.1443-9.78822.86643.4683
24.1004-0.9744-2.66231.58912.09464.6162-0.0647-0.1513-0.22990.27980.00170.02920.2874-0.05480.06790.21160.0166-0.03330.14890.02570.1272-15.3376-2.4778.4911
36.37480.9583-0.33787.16810.03257.4870.0991-0.0603-0.104-0.0323-0.04340.43850.1949-0.4456-0.07390.1262-0.0027-0.00540.144-0.00190.1426-24.5014-3.1176-0.6024
41.313-0.3804-0.05551.39050.62661.3938-0.0241-0.012-0.078-0.02680.0535-0.03650.14760.1159-0.02540.18190.028-0.00380.17590.00840.1435-12.12815.07830.6706
53.25440.20353.2561.15340.76285.02170.11740.1838-0.1525-0.08340.0925-0.03740.21140.204-0.18430.15350.00830.02330.1586-0.01240.1741-12.6582-5.5806-15.5915
66.277-7.02940.41269.3045-0.750.01150.03090.35040.113-0.1291-0.0785-0.0708-0.09010.09830.05840.21070.0001-0.0160.19280.01880.1292-18.7711.7464-21.8463
77.9786-2.5939-3.02291.55751.51213.026-0.16840.0540.05150.02910.0441-0.0077-0.07260.00630.10560.1772-0.0246-0.02420.10180.02430.164-20.695314.9913-8.4109
83.9883-3.89270.84854.717-0.93671.6034-0.0679-0.06260.6526-0.03690.0984-0.2777-0.1955-0.1484-0.04420.2602-0.0312-0.02890.19310.01860.2446-19.798424.4493-12.2234
90.8336-0.2430.20133.4366-0.20361.1341-00.0504-0.0525-0.04970.00540.02930.07290.03470.00350.15760.0072-0.00730.1764-0.01380.1331-18.01070.5635-14.4964
101.4742-2.02610.43252.9348-0.22853.96460.05430.3331-0.2395-0.0330.0454-0.72050.0530.9363-0.14740.23320.0388-0.03830.375-0.05470.3031-3.9775-10.2495-16.3506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 47 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 76 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 117 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 147 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 170 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 171 through 217 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 218 through 232 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 233 through 276 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 277 through 296 )A0

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