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- PDB-6p7f: Human ABCC6 NBD2 R1459D mutant in Apo state -

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Basic information

Entry
Database: PDB / ID: 6p7f
TitleHuman ABCC6 NBD2 R1459D mutant in Apo state
ComponentsMultidrug resistance-associated protein 6
KeywordsTRANSPORT PROTEIN / ABCC6 / NBD2 / Apo state / ATP-Binding Cassette transporter C6 / nucleotide binding domain 2
Function / homology
Function and homology information


Defective ABCC6 causes PXE / inorganic diphosphate transport / inhibition of non-skeletal tissue mineralization / ATP transport / response to sodium phosphate / leukotriene transport / ABC-type glutathione-S-conjugate transporter / phosphate ion homeostasis / ABC-type glutathione S-conjugate transporter activity / : ...Defective ABCC6 causes PXE / inorganic diphosphate transport / inhibition of non-skeletal tissue mineralization / ATP transport / response to sodium phosphate / leukotriene transport / ABC-type glutathione-S-conjugate transporter / phosphate ion homeostasis / ABC-type glutathione S-conjugate transporter activity / : / intracellular phosphate ion homeostasis / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled transmembrane transporter activity / response to magnesium ion / ABC-type transporter activity / ATP metabolic process / calcium ion homeostasis / visual perception / basal plasma membrane / transmembrane transport / ABC-family protein mediated transport / gene expression / basolateral plasma membrane / response to xenobiotic stimulus / endoplasmic reticulum membrane / ATP hydrolysis activity / extracellular region / nucleoplasm / ATP binding / plasma membrane
Similarity search - Function
Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / 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. ...Multi drug resistance-associated protein / : / ABC transporter TMD0 domain / : / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-binding cassette sub-family C member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85003990159 Å
AuthorsZheng, A. / Thibodeau, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122091 United States
CitationJournal: To Be Published
Title: Structures of human ABCC6 NBD1 and NBD2
Authors: Zheng, A. / Thibodeau, P.H.
History
DepositionJun 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0992
Polymers27,0031
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.340, 99.340, 84.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Multidrug resistance-associated protein 6 / ATP-binding cassette sub-family C member 6 / Anthracycline resistance-associated protein / Multi- ...ATP-binding cassette sub-family C member 6 / Anthracycline resistance-associated protein / Multi-specific organic anion transporter E / MOAT-E


Mass: 27003.279 Da / Num. of mol.: 1 / Fragment: residues 1254-1503 / Mutation: R1459D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCC6, ARA, MRP6 / Production host: Escherichia coli (E. coli) / References: UniProt: O95255
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
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: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 1.6 M Ammonium sulfate, 10% dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.85→44.43 Å / Num. obs: 10293 / % possible obs: 99.6 % / Redundancy: 26.3 % / Biso Wilson estimate: 61.5039316441 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.037 / Rrim(I) all: 0.193 / Net I/σ(I): 17.7
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 28.17 % / Rmerge(I) obs: 2.082 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1000 / CC1/2: 0.817 / Rpim(I) all: 0.392 / Rrim(I) all: 2.119 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZR

6bzr


Resolution: 2.85003990159→44.426198577 Å / SU ML: 0.51345447238 / Cross valid method: FREE R-VALUE / σ(F): 1.34350785683 / Phase error: 30.8001384992
RfactorNum. reflection% reflection
Rfree0.289210880334 1026 10.003900156 %
Rwork0.261702063763 --
obs0.264349352919 10256 99.6695821186 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.8948860625 Å2
Refinement stepCycle: LAST / Resolution: 2.85003990159→44.426198577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 5 0 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009315101689471918
X-RAY DIFFRACTIONf_angle_d1.128865998942597
X-RAY DIFFRACTIONf_chiral_restr0.0691716720655299
X-RAY DIFFRACTIONf_plane_restr0.0059686685782335
X-RAY DIFFRACTIONf_dihedral_angle_d23.481607178711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.00030.4621862204681440.408200671921291X-RAY DIFFRACTION99.7913769124
3.0003-3.18820.3445632825151420.3019383503161286X-RAY DIFFRACTION100
3.1882-3.43430.323702594761450.2750004273281302X-RAY DIFFRACTION99.7243280496
3.4343-3.77970.29098121761430.2615559129381284X-RAY DIFFRACTION99.3732590529
3.7797-4.32620.2508718574921460.2274517589621318X-RAY DIFFRACTION99.727520436
4.3262-5.44910.2437031845521480.2332657022711331X-RAY DIFFRACTION99.462004035
5.4491-44.43160.2931337285591580.2654470505241418X-RAY DIFFRACTION99.6837444655

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