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- PDB-2rdd: X-ray crystal structure of AcrB in complex with a novel transmemb... -

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Basic information

Entry
Database: PDB / ID: 2rdd
TitleX-ray crystal structure of AcrB in complex with a novel transmembrane helix.
Components
  • Acriflavine resistance protein B
  • UPF0092 membrane protein yajC
KeywordsMembrane protein/TRANSPORT PROTEIN / DRUG RESISTANCE / MULTIDRUG EFFLUX / TRANSPORTER / ANTIPORTER / MEMBRANE PROTEIN / NOVEL TRANSMEMBRANE HELIX / ACRB / YAJC / Inner membrane / Membrane protein-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


cell envelope Sec protein transport complex / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / plasma membrane => GO:0005886 / protein transport / outer membrane-bounded periplasmic space / membrane ...cell envelope Sec protein transport complex / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / plasma membrane => GO:0005886 / protein transport / outer membrane-bounded periplasmic space / membrane / identical protein binding / plasma membrane
Similarity search - Function
Preprotein translocase YajC / Preprotein translocase subunit / Preprotein translocase subunit / 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 ...Preprotein translocase YajC / Preprotein translocase subunit / Preprotein translocase subunit / 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-AIC / Sec translocon accessory complex subunit YajC / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTornroth-Horsefield, S. / Gourdon, P. / Horsefield, R. / Neutze, R.
CitationJournal: Structure / Year: 2007
Title: Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.
Authors: Tornroth-Horsefield, S. / Gourdon, P. / Horsefield, R. / Brive, L. / Yamamoto, N. / Mori, H. / Snijder, A. / Neutze, R.
History
DepositionSep 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Acriflavine resistance protein B
B: UPF0092 membrane protein yajC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8114
Polymers118,1132
Non-polymers6992
Water0
1
A: Acriflavine resistance protein B
B: UPF0092 membrane protein yajC
hetero molecules

A: Acriflavine resistance protein B
B: UPF0092 membrane protein yajC
hetero molecules

A: Acriflavine resistance protein B
B: UPF0092 membrane protein yajC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,43412
Polymers354,3386
Non-polymers2,0966
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.097, 145.097, 511.644
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: 113665.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: JM109 / References: UniProt: P31224
#2: Protein/peptide UPF0092 membrane protein yajC


Mass: 4447.506 Da / Num. of mol.: 1 / Fragment: UNP residues 19-55 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: JM109 / References: UniProt: P0ADZ7
#3: Chemical ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID / Ampicillin


Mass: 349.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3O4S / 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: 4.45 Å3/Da / Density % sol: 72.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14-28% PEG1000 or PEG1500, 0.1M Tris, 0.1M LiSO4, 18mM n-Octyl-beta-D-Thioglucopyranoside and 20% 1,2,3-heptanetriol as an additive, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.5→72.55 Å / Num. all: 23777 / Num. obs: 23532 / % possible obs: 88 % / Redundancy: 3.9 % / Biso Wilson estimate: 104.2 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 5.9
Reflection shellResolution: 3.5→3.72 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3454 / Rsym value: 0.553 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IWG

1iwg


Resolution: 3.5→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Polyalanine model of Chain B (YajC) except for five residues that showed positive side chain electron density(above 3.0 sigma level) in the Fobs-Fcalc density map calculated with an all-polyalanine model.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1181 -Random
Rwork0.279 ---
obs-23525 88 %-
Displacement parametersBiso mean: 65.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a1.04 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7980 0 48 0 8028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.3

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