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- PDB-6a6n: Crystal structure of an inward-open apo state of the eukaryotic A... -

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Basic information

Entry
Database: PDB / ID: 6a6n
TitleCrystal structure of an inward-open apo state of the eukaryotic ABC multidrug transporter CmABCB1
ComponentsATP-binding cassette, sub-family B, member 1
KeywordsTRANSPORT PROTEIN / ALPHA-HELICAL
Function / homology
Function and homology information


oligopeptide export from mitochondrion / ABC-type oligopeptide transporter activity / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / metal ion binding
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
Probable ATP-dependent transporter ycf16
Similarity search - Component
Biological speciesCyanidioschyzon merolae strain 10D (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsKato, H. / Nakatsu, T. / Kodan, A.
CitationJournal: Nat Commun / Year: 2019
Title: Inward- and outward-facing X-ray crystal structures of homodimeric P-glycoprotein CmABCB1.
Authors: Kodan, A. / Yamaguchi, T. / Nakatsu, T. / Matsuoka, K. / Kimura, Y. / Ueda, K. / Kato, H.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: ATP-binding cassette, sub-family B, member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0996
Polymers66,0471
Non-polymers2,0525
Water23413
1
A: ATP-binding cassette, sub-family B, member 1
hetero molecules

A: ATP-binding cassette, sub-family B, member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,19812
Polymers132,0932
Non-polymers4,10510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area13890 Å2
ΔGint-102 kcal/mol
Surface area53100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.690, 179.690, 157.666
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ATP-binding cassette, sub-family B, member 1


Mass: 66046.609 Da / Num. of mol.: 1 / Mutation: Q147A, T381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae strain 10D (eukaryote)
Strain: 10D / Gene: CYME_CMD148C / Plasmid: pABC3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD1-8u- / References: UniProt: M1VAN7
#2: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.85 Å3/Da / Density % sol: 68.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 14% PEG 2000 MME, 100mM magnesium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.02→47.14 Å / Num. obs: 19238 / % possible obs: 99.6 % / Redundancy: 9.98 % / Rsym value: 0.102 / Net I/σ(I): 14.3
Reflection shellResolution: 3.02→3.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WME

3wme


Resolution: 3.02→47.14 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.839 / SU B: 22.948 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R: 7.819 / ESU R Free: 0.422 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27473 962 5 %RANDOM
Rwork0.22567 ---
obs0.22823 18276 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 90.306 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 3.02→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 71 13 4560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194629
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9776266
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8155586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99123.037191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20815753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9581536
X-RAY DIFFRACTIONr_chiral_restr0.350.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213425
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.6529.0332348
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.1313.5542932
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.8879.1972279
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined18.90684.57519274
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.022→3.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 68 -
Rwork0.447 1303 -
obs--96.82 %

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