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- PDB-4k7q: Crystal Structure of AcrB Complexed with Linezolid at 3.5 Resolution -

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Basic information

Entry
Database: PDB / ID: 4k7q
TitleCrystal Structure of AcrB Complexed with Linezolid at 3.5 Resolution
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN/ANTIBIOTIC / inner membrane resistance-nodulation-cell division efflux pump / MEMBRANE PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ZLD / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHung, L.W. / Kim, H.B. / Murakami, S. / Gupta, G. / Kim, C.Y. / Terwilliger, T.C.
CitationJournal: J.Struct.Funct.Genom. / Year: 2013
Title: Crystal structure of AcrB complexed with linezolid at 3.5 Angstrom resolution.
Authors: Hung, L.W. / Kim, H.B. / Murakami, S. / Gupta, G. / Kim, C.Y. / Terwilliger, T.C.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Non-polymer description
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5552
Polymers114,2181
Non-polymers3371
Water00
1
A: Acriflavine resistance protein B
hetero molecules

A: Acriflavine resistance protein B
hetero molecules

A: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,6656
Polymers342,6533
Non-polymers1,0123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area19850 Å2
ΔGint-84 kcal/mol
Surface area112220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.685, 144.685, 519.357
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Acriflavine resistance protein B


Mass: 114217.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Chemical ChemComp-ZLD / N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide / Linezolid


Mass: 337.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20FN3O4 / Comment: antibiotic*YM

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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: 4.58 Å3/Da / Density % sol: 73.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M NaCl 8% PEG 4k 0.1M NaPhosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 26687 / Num. obs: 26634 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 2.26 / Rsym value: 0.788 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→46.591 Å / SU ML: 0.49 / σ(F): 1.34 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3036 1788 6.96 %RANDOM
Rwork0.2513 ---
all0.255 25704 --
obs0.255 25678 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→46.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7676 0 24 0 7700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037843
X-RAY DIFFRACTIONf_angle_d0.76710650
X-RAY DIFFRACTIONf_dihedral_angle_d14.0762831
X-RAY DIFFRACTIONf_chiral_restr0.0481259
X-RAY DIFFRACTIONf_plane_restr0.0051357
LS refinement shellResolution: 3.5→3.62 Å
RfactorNum. reflection% reflection
Rfree0.4399 107 -
Rwork0.3589 1041 -
obs-1576 90.1 %
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)
11.63680.2875-0.040.59010.52642.13930.12750.19450.1995-0.03710.3006-0.1075-0.06820.0568-0.00010.65460.0873-0.01340.93530.01091.070457.481741.7101325.3785
20.04370.12591.69530.8861-0.42450.22180.10110.47110.0292-0.2371-0.33450.00520.43490.2957-0.00310.84270.19310.07451.57690.13880.785552.024927.4286331.9973
3-0.23930.045-0.00461.1124-0.28240.67920.12240.40470.3514-0.5817-0.0520.0340.09680.446501.0382-0.1504-0.21911.87730.44491.411239.053843.6717299.1903
40.34190.16430.23330.65850.13070.2186-0.5180.5551.93690.26090.78911.5002-0.53570.01070.01351.23570.104-0.36621.29230.18581.421641.208459.6993330.5081
50.50270.2757-0.55360.79980.26172.1767-0.01160.39160.3212-0.3736-0.09910.4975-0.8439-0.6402-00.90010.2873-0.18361.3120.09011.193945.110953.0051314.8585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 391 )
3X-RAY DIFFRACTION3chain 'A' and (resid 392 through 657 )
4X-RAY DIFFRACTION4chain 'A' and (resid 658 through 708 )
5X-RAY DIFFRACTION5chain 'A' and (resid 709 through 1036 )

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