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- PDB-6bzr: Human ABCC6 NBD2 in ADP-bound state -

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Basic information

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


Defective ABCC6 causes PXE / inorganic diphosphate transport / ATP transport / inhibition of non-skeletal tissue mineralization / leukotriene transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / intracellular phosphate ion homeostasis / response to sodium phosphate / ATPase-coupled inorganic anion transmembrane transporter activity ...Defective ABCC6 causes PXE / inorganic diphosphate transport / ATP transport / inhibition of non-skeletal tissue mineralization / leukotriene transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / intracellular phosphate ion homeostasis / response to sodium phosphate / ATPase-coupled inorganic anion transmembrane transporter activity / phosphate ion homeostasis / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / response to magnesium ion / ATPase-coupled transmembrane transporter activity / calcium ion homeostasis / ATP metabolic process / visual perception / basal plasma membrane / ABC-family proteins mediated transport / transmembrane transport / gene expression / basolateral plasma membrane / response to xenobiotic stimulus / endoplasmic reticulum membrane / ATP hydrolysis activity / extracellular region / nucleoplasm / ATP binding / membrane / plasma membrane
Similarity search - Function
Multi drug resistance-associated protein / 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. ...Multi drug resistance-associated protein / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CITRIC ACID / ATP-binding cassette sub-family C member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.79999446301 Å
AuthorsZheng, A. / Thibodeau, P.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK083284 United States
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
DepositionDec 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

Downloads & links

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Assembly

Deposited unit
B: Multidrug resistance-associated protein 6
A: Multidrug resistance-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5046
Polymers54,2652
Non-polymers1,2394
Water82946
1
B: Multidrug resistance-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7523
Polymers27,1321
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Multidrug resistance-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7523
Polymers27,1321
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.760, 93.120, 64.170
Angle α, β, γ (deg.)90.000, 112.497, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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: 27132.463 Da / Num. of mol.: 2 / Fragment: residues 622-859
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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M Sodium Citrate pH 6.2, 12.5% PEG 4000, 18% propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.79999446301→49.3420740866 Å / Num. obs: 29279 / % possible obs: 99.4 % / Redundancy: 4.36 % / Biso Wilson estimate: 40.2937292237 Å2 / CC1/2: 0.934 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 1.93 / Num. unique obs: 2127 / CC1/2: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GD7

3gd7


Resolution: 2.79999446301→49.3420740866 Å / SU ML: 0.477631922965 / Cross valid method: FREE R-VALUE / σ(F): 1.34747057572 / Phase error: 28.4256620556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264066464625 2817 9.6340629275 %
Rwork0.2309000121 26423 -
obs0.234182414144 29240 99.6489793136 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.079167556 Å2
Refinement stepCycle: LAST / Resolution: 2.79999446301→49.3420740866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 80 46 3714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01449613472353724
X-RAY DIFFRACTIONf_angle_d1.233531091625045
X-RAY DIFFRACTIONf_chiral_restr0.0923565489021585
X-RAY DIFFRACTIONf_plane_restr0.00575077350237638
X-RAY DIFFRACTIONf_dihedral_angle_d20.84138376341385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.84830.3578164872471430.3413913143871285X-RAY DIFFRACTION99.9300209937
2.8483-2.90010.3984682628171470.3539938106441351X-RAY DIFFRACTION99.8666666667
2.9001-2.95580.4144829146811390.2977720538671308X-RAY DIFFRACTION100
2.9558-3.01620.3611179704531320.305322326611354X-RAY DIFFRACTION100
3.0162-3.08170.3543547953461480.2884590494361309X-RAY DIFFRACTION99.9314128944
3.0817-3.15340.3688930604281260.2751205542481319X-RAY DIFFRACTION100
3.1534-3.23220.2968499164871530.2671568005351330X-RAY DIFFRACTION99.9326145553
3.2322-3.31960.3186988949481340.2661882405331312X-RAY DIFFRACTION100
3.3196-3.41730.3001366385461520.2553049451991334X-RAY DIFFRACTION100
3.4173-3.52760.2618739830411360.2302297630341347X-RAY DIFFRACTION99.9326145553
3.5276-3.65360.2477432342941590.2179483352411263X-RAY DIFFRACTION99.7894736842
3.6536-3.79980.2217447855391300.2151932742961354X-RAY DIFFRACTION99.5305164319
3.7998-3.97270.2817096628011400.2103100906961346X-RAY DIFFRACTION99.3315508021
3.9727-4.1820.2570120762381400.2195936433181316X-RAY DIFFRACTION99.5896032832
4.182-4.44390.2791271070071340.194918263441300X-RAY DIFFRACTION99.3074792244
4.4439-4.78680.2355675603291500.192115903751335X-RAY DIFFRACTION99.5975855131
4.7868-5.2680.20539880951350.1970606382971322X-RAY DIFFRACTION99.7262149213
5.268-6.02910.2218269696171350.2050042840971333X-RAY DIFFRACTION99.7282608696
6.0291-7.59160.1962676887241430.2140130290561321X-RAY DIFFRACTION99.4565217391
7.5916-49.34970.1824270468311410.1971644868911284X-RAY DIFFRACTION97.3360655738

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