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- PDB-5drq: Crystal structure of the Pseudomonas aeruginosa LpxC/LPC-040 complex -

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Basic information

Entry
Database: PDB / ID: 5drq
TitleCrystal structure of the Pseudomonas aeruginosa LpxC/LPC-040 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 / membrane / 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-5EM / NITRATE ION / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 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)35,46633
Polymers33,1471
Non-polymers2,31932
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.433, 74.001, 88.629
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-5EM / N-[(2S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]benzamide


Mass: 390.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O3
#4: Chemical...
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
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: Dec 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 46824 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.356 / Net I/av σ(I): 37.24 / Net I/σ(I): 19.8 / Num. measured all: 309789
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.63-1.666.30.40323141.08399.6
1.66-1.696.40.34222971.105100
1.69-1.726.40.28923331.106100
1.72-1.756.50.25723161.117100
1.75-1.796.50.21623001.146100
1.79-1.836.50.18223071.188100
1.83-1.886.50.15423351.21499.9
1.88-1.936.50.13223291.25499.9
1.93-1.986.60.11923101.53399.8
1.98-2.056.60.09323131.29699.7
2.05-2.126.70.07623051.3399.6
2.12-2.26.70.0723421.34599.5
2.2-2.36.10.07822982.15698.5
2.3-2.426.70.06123481.4499.7
2.42-2.576.90.05523571.35399.9
2.57-2.7770.0523361.377100
2.77-3.047.10.04723781.448100
3.04-3.487.10.04223831.492100
3.48-4.376.40.0423851.60598.3
4.37-506.70.0425381.51699.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3E

3p3e


Resolution: 1.63→17.871 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 2187 5.04 %
Rwork0.1695 41183 -
obs0.1712 43370 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.66 Å2 / Biso mean: 26.5891 Å2 / Biso min: 13.56 Å2
Refinement stepCycle: final / Resolution: 1.63→17.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 147 263 2682
Biso mean--37.62 36.58 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092496
X-RAY DIFFRACTIONf_angle_d1.1633359
X-RAY DIFFRACTIONf_chiral_restr0.052374
X-RAY DIFFRACTIONf_plane_restr0.006457
X-RAY DIFFRACTIONf_dihedral_angle_d11.681893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6305-1.66590.29321410.25932399254094
1.6659-1.70460.26091500.226325382688100
1.7046-1.74720.24991370.198325892726100
1.7472-1.79440.21181210.184425432664100
1.7944-1.84720.20081410.180925642705100
1.8472-1.90670.22071380.178725442682100
1.9067-1.97480.23031200.185926042724100
1.9748-2.05380.19791400.167925622702100
2.0538-2.14710.1941140.153826052719100
2.1471-2.26010.20121460.160525782724100
2.2601-2.40140.18881460.163925772723100
2.4014-2.58630.17891140.175726082722100
2.5863-2.84560.23281320.184726072739100
2.8456-3.25520.21011530.18352593274699
3.2552-4.09310.18441360.14612619275599
4.0931-17.87230.19081580.15852653281196
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)
12.0712.10120.98024.6024-0.99613.3853-0.13290.1120.0557-0.21280.29310.02990.0226-0.1689-0.13740.11030.05810.00810.1212-0.02690.15669.64752.8522-3.5555
22.99680.4383-1.65461.4791-1.31663.68410.00380.0511-0.1571-0.2908-0.01780.08940.29830.04530.03080.2174-0.0038-0.0220.1369-0.01580.137914.7959-2.4726-8.6146
34.3619-0.92660.17557.17880.73127.92560.13480.04960.01420.0092-0.0316-0.43640.13560.3483-0.14160.11020.02390.00180.1443-0.00070.150724.5752-2.84270.6017
40.98530.1528-0.50391.298-0.58951.4458-0.0147-0.0151-0.0533-0.02240.02940.04490.1381-0.0344-0.02170.1828-0.0094-0.01430.1839-0.00040.154311.90185.0493-0.6005
53.14490.33623.02142.1839-0.72194.99060.114-0.0445-0.21670.16480.1121-0.00560.1506-0.0769-0.21950.150.01230.03710.16320.01460.156312.7897-5.447815.8796
66.86375.9044-0.01465.13660.01660.00520.084-0.36570.13390.1545-0.15070.1117-0.0866-0.00720.05090.2021-0.0070.00180.1804-0.01970.151618.642711.832521.9441
76.87491.8459-2.84331.6975-0.96732.9865-0.0251-0.12320.0127-0.0166-0.0297-0.0315-0.11180.08750.03360.17230.0097-0.01020.0972-0.00680.151821.367914.98268.644
82.63153.63391.42135.95241.26773.08040.04130.02920.42540.0747-0.01270.2637-0.25630.142-0.04440.18540.0240.00820.1915-0.00260.2119.573424.233612.3279
90.48630.2202-0.11623.4943-0.07010.83640.0169-0.0122-0.05780.0352-0.0168-0.05460.11350.02870.00450.18180.0026-0.01460.19450.00150.148317.76620.373514.3796
108.5588-3.29483.55245.91470.22316.88020.2413-0.2878-0.0431-0.1387-0.12650.5495-0.0651-0.9148-0.06740.224-0.0504-0.00380.29140.0920.26693.9691-10.121516.3863
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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