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- PDB-7cz9: Crystal structure of multidrug efflux transporter OqxB from Klebs... -

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Basic information

Entry
Database: PDB / ID: 7cz9
TitleCrystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae
ComponentsEfflux pump membrane transporter
KeywordsMEMBRANE PROTEIN / Multidrug efflux transporter / Drug efflux transporter / Membrane transporter / RND transporter / Secondary-active transporter / Multidrug resistance
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / PHOSPHATIDYLETHANOLAMINE / Efflux pump membrane transporter
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMurakami, S. / Okada, U. / Yamashita, E.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02386 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05396 Japan
Japan Society for the Promotion of Science (JSPS)JP18K06079 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae.
Authors: Bharatham, N. / Bhowmik, P. / Aoki, M. / Okada, U. / Sharma, S. / Yamashita, E. / Shanbhag, A.P. / Rajagopal, S. / Thomas, T. / Sarma, M. / Narjari, R. / Nagaraj, S. / Ramachandran, V. / ...Authors: Bharatham, N. / Bhowmik, P. / Aoki, M. / Okada, U. / Sharma, S. / Yamashita, E. / Shanbhag, A.P. / Rajagopal, S. / Thomas, T. / Sarma, M. / Narjari, R. / Nagaraj, S. / Ramachandran, V. / Katagihallimath, N. / Datta, S. / Murakami, S.
History
DepositionSep 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter
D: Efflux pump membrane transporter
E: Efflux pump membrane transporter
F: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)722,462122
Polymers676,2876
Non-polymers46,175116
Water52,9642940
1
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,68059
Polymers338,1433
Non-polymers21,53656
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Efflux pump membrane transporter
E: Efflux pump membrane transporter
F: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,78363
Polymers338,1433
Non-polymers24,63960
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.947, 128.780, 137.262
Angle α, β, γ (deg.)91.28, 90.01, 103.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Efflux pump membrane transporter / OqxB


Mass: 112714.461 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): B / BL21-DE3 / References: UniProt: U5U6L7
#2: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2940 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, sodium chloride, Glycerol, 2-(N-morpholino)ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2019
RadiationMonochromator: two Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→43.28 Å / Num. obs: 709740 / % possible obs: 96.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 34205 / CC1/2: 0.48 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XDSVer. Mar 15, 2019data reduction
XSCALEVer. Mar 15, 2019data scaling
PHASER(1.18_3845: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DX5

4dx5


Resolution: 1.85→43.28 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 35722 5.04 %
Rwork0.1802 --
obs0.1821 709314 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47503 0 2921 2940 53364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01851441
X-RAY DIFFRACTIONf_angle_d1.40869714
X-RAY DIFFRACTIONf_dihedral_angle_d13.6647848
X-RAY DIFFRACTIONf_chiral_restr0.098468
X-RAY DIFFRACTIONf_plane_restr0.0098528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.389811660.359922003X-RAY DIFFRACTION95
1.87-1.890.372911750.339722383X-RAY DIFFRACTION96
1.89-1.920.352612060.317622238X-RAY DIFFRACTION96
1.92-1.940.326412250.29322366X-RAY DIFFRACTION96
1.94-1.970.322511600.27522413X-RAY DIFFRACTION96
1.97-1.990.3111760.264822309X-RAY DIFFRACTION96
1.99-2.020.292912190.253922423X-RAY DIFFRACTION96
2.02-2.050.279811190.234822414X-RAY DIFFRACTION97
2.05-2.080.263911770.227922416X-RAY DIFFRACTION97
2.08-2.120.252111440.204522604X-RAY DIFFRACTION97
2.12-2.150.246511640.200322413X-RAY DIFFRACTION97
2.15-2.190.243511660.190822450X-RAY DIFFRACTION97
2.19-2.240.235512390.185522426X-RAY DIFFRACTION97
2.24-2.280.231111720.180922518X-RAY DIFFRACTION97
2.28-2.330.224812150.182522524X-RAY DIFFRACTION97
2.33-2.390.23412400.176722577X-RAY DIFFRACTION97
2.39-2.440.227812290.176122454X-RAY DIFFRACTION97
2.44-2.510.224812410.176122508X-RAY DIFFRACTION97
2.51-2.580.225412030.172822615X-RAY DIFFRACTION97
2.58-2.670.222411820.170422509X-RAY DIFFRACTION97
2.67-2.760.214112050.17122575X-RAY DIFFRACTION97
2.76-2.870.229912670.177722492X-RAY DIFFRACTION97
2.87-30.222812000.172122608X-RAY DIFFRACTION97
3-3.160.226411700.175822570X-RAY DIFFRACTION97
3.16-3.360.213811440.170522658X-RAY DIFFRACTION97
3.36-3.620.19811500.165122617X-RAY DIFFRACTION97
3.62-3.980.195711370.165322449X-RAY DIFFRACTION97
3.98-4.560.183311850.155222353X-RAY DIFFRACTION96
4.56-5.740.183513000.163822293X-RAY DIFFRACTION97
5.74-43.280.20411460.182222414X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 1.0787 Å / Origin y: 80.4547 Å / Origin z: -14.4714 Å
111213212223313233
T0.2312 Å2-0.0001 Å20.0067 Å2-0.2427 Å2-0.0344 Å2--0.2635 Å2
L0.09 °2-0.0063 °20.0232 °2-0.0539 °2-0.0207 °2--0.1784 °2
S-0.0064 Å °-0.0094 Å °0.0007 Å °-0.0073 Å °0.0087 Å °-0.0009 Å °-0.007 Å °-0.0069 Å °-0 Å °
Refinement TLS groupSelection details: all

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