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- PDB-4xwk: P-glycoprotein co-crystallized with BDE-100 -

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Basic information

Entry
Database: PDB / ID: 4xwk
TitleP-glycoprotein co-crystallized with BDE-100
ComponentsMultidrug resistance protein 1A
KeywordsHYDROLASE / membrane protein / transporter
Function / homology
Function and homology information


hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / negative regulation of sensory perception of pain / regulation of intestinal absorption ...hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / negative regulation of sensory perception of pain / regulation of intestinal absorption / response to quercetin / cellular response to external biotic stimulus / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / terpenoid transport / ceramide floppase activity / response to glycoside / floppase activity / ceramide translocation / establishment of blood-retinal barrier / protein localization to bicellular tight junction / response to alcohol / ABC-family proteins mediated transport / response to thyroxine / establishment of blood-brain barrier / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / cellular response to L-glutamate / intercellular canaliculus / export across plasma membrane / ABC-type xenobiotic transporter / response to vitamin D / P-type phospholipid transporter / response to vitamin A / ABC-type xenobiotic transporter activity / intestinal absorption / response to glucagon / phospholipid translocation / cellular response to antibiotic / cellular hyperosmotic salinity response / maintenance of blood-brain barrier / cellular response to alkaloid / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / cellular response to estradiol stimulus / response to progesterone / female pregnancy / brush border membrane / placenta development / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,4-dibromophenyl 2,4,6-tribromophenyl ether / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMcGrath, A.P. / Rees, S.D. / Chang, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)5R01ES021985-03 United States
CitationJournal: Sci Adv / Year: 2016
Title: Global marine pollutants inhibit P-glycoprotein: Environmental levels, inhibitory effects, and cocrystal structure.
Authors: Nicklisch, S.C. / Rees, S.D. / McGrath, A.P. / Gokirmak, T. / Bonito, L.T. / Vermeer, L.M. / Cregger, C. / Loewen, G. / Sandin, S. / Chang, G. / Hamdoun, A.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4852
Polymers141,9201
Non-polymers5651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.000, 138.160, 185.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Multidrug resistance protein 1A / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 3 / P-glycoprotein 3


Mass: 141919.953 Da / Num. of mol.: 1 / Mutation: N83Q, N87Q, N90Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Plasmid: pPICZ / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P21447, xenobiotic-transporting ATPase
#2: Chemical ChemComp-4C8 / 2,4-dibromophenyl 2,4,6-tribromophenyl ether


Mass: 564.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H5Br5O

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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: 4.15 Å3/Da / Density % sol: 70.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: PEG 600, Li2O4S, HEPES, EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.91929 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91929 Å / Relative weight: 1
ReflectionResolution: 3.5→92.57 Å / Num. obs: 29261 / % possible obs: 99.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 139.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.04 / Net I/σ(I): 10.2 / Num. measured all: 156577 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.5-3.715.40.8282.22524346950.7540.3899.9
10.5-92.574.90.04625.2559011450.9970.02394.6

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Processing

Software
NameVersionClassification
MOSFLM7.1.0data reduction
Aimless0.3.5data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Q9H

4q9h


Resolution: 3.5→92.57 Å / SU ML: 0.73 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 34.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 2757 5.03 %Random selection
Rwork0.2626 52042 --
obs0.2636 29202 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 342.02 Å2 / Biso mean: 153.0536 Å2 / Biso min: 82.52 Å2
Refinement stepCycle: final / Resolution: 3.5→92.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9164 0 18 0 9182
Biso mean--178.16 --
Num. residues----1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069352
X-RAY DIFFRACTIONf_angle_d0.98812642
X-RAY DIFFRACTIONf_chiral_restr0.0381453
X-RAY DIFFRACTIONf_plane_restr0.0041604
X-RAY DIFFRACTIONf_dihedral_angle_d14.2683398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.56040.43741250.41122683280899
3.5604-3.62520.40911310.368425842715100
3.6252-3.69490.39571620.34562626278899
3.6949-3.77030.37471160.35122615273199
3.7703-3.85230.38951470.31612623277099
3.8523-3.94190.38611170.30312639275699
3.9419-4.04050.29451500.28952594274499
4.0405-4.14980.31061530.29242593274699
4.1498-4.27190.27141330.27652629276299
4.2719-4.40980.30821390.252625276499
4.4098-4.56740.26061000.24682637273799
4.5674-4.75020.28741170.24142627274499
4.7502-4.96640.23321280.23472630275899
4.9664-5.22820.28321470.24882583273099
5.2282-5.55570.33221450.26062597274298
5.5557-5.98460.29511550.28332565272098
5.9846-6.58670.36061430.27942593273698
6.5867-7.53950.29151750.25752543271898
7.5395-9.49750.19951430.20172566270998
9.4975-92.60740.23441310.25392490262194

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