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- PDB-2gfp: Structure of the Multidrug Transporter EmrD from Escherichia coli -

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Open data


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Basic information

Entry
Database: PDB / ID: 2gfp
TitleStructure of the Multidrug Transporter EmrD from Escherichia coli
ComponentsMultidrug resistance protein DMultiple drug resistance
KeywordsMEMBRANE PROTEIN / Multidrug Transporter
Function / homology
Function and homology information


xenobiotic transmembrane transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transmembrane transporter activity / plasma membrane => GO:0005886 / plasma membrane
Similarity search - Function
Multidrug resistance protein D / Multidrug resistance protein D / Multidrug resistance protein / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Multidrug resistance protein D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsYin, Y. / He, X. / Szewczyk, P. / Nguyen, T. / Chang, G.
CitationJournal: Science / Year: 2006
Title: Structure of the multidrug transporter EmrD from Escherichia coli
Authors: Yin, Y. / He, X. / Szewczyk, P. / Nguyen, T. / Chang, G.
History
DepositionMar 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug resistance protein D
B: Multidrug resistance protein D


Theoretical massNumber of molelcules
Total (without water)80,0282
Polymers80,0282
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.500, 124.500, 109.400
Angle α, β, γ (deg.)90.00, 110.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Multidrug resistance protein D / Multiple drug resistance / EmrD


Mass: 40013.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: emrD / Production host: Escherichia coli (E. coli) / References: UniProt: P31442

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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: 5.5 Å3/Da / Density % sol: 74.61 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.4
Details: 20-21% PEG 400, 50 mM sodium citrate, pH 4.4 and 4.8, and 50 mM KCl, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.03840,1.04040
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03841
21.04041
ReflectionResolution: 3.5→50 Å / Num. all: 16781 / Num. obs: 13425 / % possible obs: 90 % / Observed criterion σ(I): 1
Reflection shellResolution: 3.5→3.7 Å / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
PHASESphasing
X-PLOR3.851refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.5→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.35 687 10 %RANDOM
Rwork0.27 ---
all0.28 7645 --
obs0.28 6879 --
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 0 0 5600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.05
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d

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