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- PDB-7szt: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -

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Basic information

Entry
Database: PDB / ID: 7szt
TitleCrystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in low pH (protonated state)
Components
  • L10 monobody
  • Multidrug resistance protein, SMR family
KeywordsTRANSPORT PROTEIN / Small Multidrug Resistance transporters / Membrane protein
Function / homologySmall drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / Dodecyldimethylphosphine oxide / Multidrug resistance protein, SMR family
Function and homology information
Biological speciesClostridiales bacterium oral taxon 876 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKermani, A.A. / Stockbridge, R.B. / Burata, O.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1845012 United States
CitationJournal: Elife / Year: 2022
Title: Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates.
Authors: Kermani, A.A. / Burata, O.E. / Koff, B.B. / Koide, A. / Koide, S. / Stockbridge, R.B.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Multidrug resistance protein, SMR family
B: Multidrug resistance protein, SMR family
C: Multidrug resistance protein, SMR family
D: Multidrug resistance protein, SMR family
E: L10 monobody
F: L10 monobody
H: L10 monobody
G: L10 monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,58810
Polymers85,0958
Non-polymers4932
Water00
1
A: Multidrug resistance protein, SMR family
B: Multidrug resistance protein, SMR family
F: L10 monobody
G: L10 monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0406
Polymers42,5484
Non-polymers4932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Multidrug resistance protein, SMR family
D: Multidrug resistance protein, SMR family
E: L10 monobody
H: L10 monobody


Theoretical massNumber of molelcules
Total (without water)42,5484
Polymers42,5484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.704, 74.323, 107.433
Angle α, β, γ (deg.)93.560, 89.710, 109.920
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Multidrug resistance protein, SMR family


Mass: 11341.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridiales bacterium oral taxon 876 (bacteria)
Gene: HMPREF1982_00479 / Production host: Escherichia coli (E. coli) / References: UniProt: U2EQ00
#2: Antibody
L10 monobody


Mass: 9931.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-9PD / Dodecyldimethylphosphine oxide / APO-12


Mass: 246.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31OP
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: 4.38 Å3/Da / Density % sol: 71.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% PEG600, sodium acetate, pH 5.0, 100 mM calciium acetate, Apo12

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.32→107.21 Å / Num. obs: 26109 / % possible obs: 80.3 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.104 / Net I/σ(I): 6.5
Reflection shellResolution: 2.32→2.67 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 1305 / CC1/2: 0.874 / Rsym value: 0.46 / % possible all: 45.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6WK8

6wk8


Resolution: 2.32→32.68 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 44.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2945 1277 4.91 %
Rwork0.2514 24748 -
obs0.2537 26085 41.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.11 Å2 / Biso mean: 37.196 Å2 / Biso min: 9.21 Å2
Refinement stepCycle: final / Resolution: 2.32→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5906 0 27 0 5933
Biso mean--39.64 --
Num. residues----769
LS refinement shellResolution: 2.32→2.405 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.8376 5 -
Rwork0.3451 127 -
obs--2 %

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