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- PDB-7bwl: Structure of antibiotic sequester from Pseudomonas aerurinosa -

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Basic information

Entry
Database: PDB / ID: 7bwl
TitleStructure of antibiotic sequester from Pseudomonas aerurinosa
ComponentsUPF0312 protein PA0423
KeywordsANTIBIOTIC / lipocalin family / antibiotic sequester / antibiotic resistance
Function / homologyUncharacterised protein family UPF0312/YceI / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / periplasmic space / extracellular space / Ubiquinone-8 / UPF0312 protein PA0423
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHong, M.
Funding supportKorea, Democratic People's Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2B6001619Korea, Democratic People's Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the Pseudomonas aeruginosa PA0423 protein and its functional implication in antibiotic sequestration.
Authors: Lee, C. / Kim, M.I. / Park, J. / Kim, J. / Oh, H. / Cho, Y. / Son, J. / Jeon, B.Y. / Ka, H. / Hong, M.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0312 protein PA0423
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5302
Polymers20,8031
Non-polymers7271
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9060 Å2
Unit cell
Length a, b, c (Å)53.338, 53.338, 134.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UPF0312 protein PA0423 / Antibiotic sequester


Mass: 20803.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA0423 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I690
#2: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: in 0.2 M Sodium chloride, 0.1 M Na/K phosphate pH 6.2, and 40 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 15025 / % possible obs: 99.7 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.026 / Rrim(I) all: 0.089 / Χ2: 1.689 / Net I/σ(I): 10.6
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.053 / Num. unique obs: 846 / CC1/2: 0.998 / Rpim(I) all: 0.018 / Rrim(I) all: 0.056 / Χ2: 1.765 / % possible all: 95.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WUB

1wub


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.597 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.231 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 503 5.2 %RANDOM
Rwork0.2179 ---
obs0.22 9240 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.46 Å2 / Biso mean: 48.194 Å2 / Biso min: 30.12 Å2
Baniso -1Baniso -2Baniso -3
1-4.88 Å2-0 Å2-0 Å2
2--4.88 Å2-0 Å2
3----9.76 Å2
Refinement stepCycle: final / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 53 50 1408
Biso mean--48.63 49.45 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191384
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9831863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81725.07765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61715227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.737156
X-RAY DIFFRACTIONr_chiral_restr0.080.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211072
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 45 -
Rwork0.277 644 -
all-689 -
obs--99.71 %
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)
12.8774-1.25531.64351.3427-0.56776.2299-0.088-0.2091-0.0742-0.12750.0662-0.12410.93440.00840.02180.28830.00730.0550.11210.00390.430512.515-6.0095.761
22.2876-0.9772-0.04461.4742-0.30993.5818-0.052-0.0376-0.1433-0.05980.07680.05770.27330.0183-0.02480.0954-0.05410.01340.049-0.05030.390810.764-1.274-3.652
37.2885-0.01622.36293.08171.49456.0396-0.09420.3041-0.1997-0.21410.0301-0.02470.30940.30910.0640.1451-0.01340.06730.03710.02350.264513.874-5.088-9.803
41.7090.334-0.19141.84331.54297.5112-0.0554-0.20340.0278-0.05020.1245-0.1445-0.03250.6039-0.06910.00270.00270.00350.0707-0.02040.32919.165-1.2050.077
520.40060.649810.886110.4469-3.501515.23810.2265-0.71350.196-0.8847-0.04750.2211-0.7026-0.7673-0.1790.24690.050.03440.0621-0.01410.215212.706-2.222-19.448
61.6848-2.07112.41583.7969-4.91519.7460.20480.07980.052-0.3026-0.1006-0.05050.4290.4348-0.10420.1006-0.01190.01550.0453-0.00290.342712.6491.717-5.505
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 38
2X-RAY DIFFRACTION2A39 - 88
3X-RAY DIFFRACTION3A89 - 118
4X-RAY DIFFRACTION4A119 - 164
5X-RAY DIFFRACTION5A165 - 169
6X-RAY DIFFRACTION6A170 - 190

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