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- PDB-7fc9: Crystal structure of CmABCB1 in lipidic mesophase revealed by LCP-SFX -

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Basic information

Entry
Database: PDB / ID: 7fc9
TitleCrystal structure of CmABCB1 in lipidic mesophase revealed by LCP-SFX
ComponentsProbable ATP-dependent transporter ycf16
KeywordsTRANSPORT PROTEIN / multi-drug exporter
Function / homology
Function and homology information


ABC-type transporter activity / chloroplast / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
Similarity search - Function
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. ...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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Probable ATP-dependent transporter ycf16
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPan, D. / Oyama, R. / Sato, T. / Nakane, T. / Mizunuma, R. / Matsuoka, K. / Joti, Y. / Tono, K. / Nango, E. / Iwata, S. ...Pan, D. / Oyama, R. / Sato, T. / Nakane, T. / Mizunuma, R. / Matsuoka, K. / Joti, Y. / Tono, K. / Nango, E. / Iwata, S. / Nakatsu, T. / Kato, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Iucrj / Year: 2022
Title: Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX.
Authors: Pan, D. / Oyama, R. / Sato, T. / Nakane, T. / Mizunuma, R. / Matsuoka, K. / Joti, Y. / Tono, K. / Nango, E. / Iwata, S. / Nakatsu, T. / Kato, H.
History
DepositionJul 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent transporter ycf16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,44916
Polymers64,1761
Non-polymers1,27315
Water2,666148
1
A: Probable ATP-dependent transporter ycf16
hetero molecules

A: Probable ATP-dependent transporter ycf16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,89832
Polymers128,3512
Non-polymers2,54730
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area21500 Å2
ΔGint-711 kcal/mol
Surface area45300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.900, 285.900, 86.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable ATP-dependent transporter ycf16


Mass: 64175.621 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 / Production host: Komagataella phaffii (fungus) / References: UniProt: M1VAN7

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Non-polymers , 6 types, 163 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Micro-crystals were generated by incubation of 50 microL LCP containing the protein and 7.7 MAG/cholesterol in a 1.5 mL tube with 0.7 mL crystallization solution containing 26-30% 1,4- ...Details: Micro-crystals were generated by incubation of 50 microL LCP containing the protein and 7.7 MAG/cholesterol in a 1.5 mL tube with 0.7 mL crystallization solution containing 26-30% 1,4-butanediol, 0.1 M Tris pH 7.9, 0.2 M zinc acetate.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.771 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.2→45.45 Å / Num. obs: 47845 / % possible obs: 100 % / Redundancy: 2149 % / CC star: 0.9996 / R split: 0.0567 / Net I/σ(I): 12.37
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 591 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 2335 / CC star: 0.7709 / R split: 0.8484 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFEL0.9.0data reduction
CrystFEL0.9.0data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6M

6a6m


Resolution: 2.2→20.001 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.18 / Average fsc free: 0.9135 / Average fsc work: 0.921 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.156 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2179 2491 5.216 %
Rwork0.1922 45270 -
all0.194 --
obs-47761 99.812 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.481 Å2
Baniso -1Baniso -2Baniso -3
1-1.473 Å2-0 Å20 Å2
2---1.672 Å2-0 Å2
3---0.199 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 48 148 4644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124567
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6236194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3320.889225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67715744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5581536
X-RAY DIFFRACTIONr_chiral_restr0.0550.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023426
X-RAY DIFFRACTIONr_nbd_refined0.1940.21717
X-RAY DIFFRACTIONr_nbtor_refined0.2850.23191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2166
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.225
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0840.21
X-RAY DIFFRACTIONr_mcbond_it2.5876.1492336
X-RAY DIFFRACTIONr_mcangle_it3.9219.2222917
X-RAY DIFFRACTIONr_scbond_it3.386.5542231
X-RAY DIFFRACTIONr_scangle_it5.4189.6733277
X-RAY DIFFRACTIONr_lrange_it7.92582.0846537
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2560.3011680.29532580.29634260.7980.8011000.278
2.256-2.3170.2811610.26932150.2733760.8390.8471000.244
2.317-2.3840.2531750.24630960.24732710.880.891000.219
2.384-2.4560.2711750.23330140.23531890.8880.8981000.201
2.456-2.5350.241790.22129110.22230900.9010.9131000.188
2.535-2.6230.2451430.20728420.20929850.9150.9231000.172
2.623-2.720.2361430.20227710.20429140.9140.9331000.171
2.72-2.8290.2311570.18526190.18727760.9320.9441000.155
2.829-2.9520.2261460.18425460.18626920.9270.9451000.158
2.952-3.0930.1821350.17624460.17625810.9580.9551000.152
3.093-3.2560.2071350.17923280.18124630.9480.9541000.162
3.256-3.4470.1941150.17122020.17223170.950.9581000.155
3.447-3.6780.1781020.16320900.16321920.9580.9621000.152
3.678-3.9610.183940.16319830.16420770.9580.9611000.158
3.961-4.3220.187990.16818010.16919000.9550.9621000.168
4.322-4.8040.206870.17816670.17917540.9510.9561000.18
4.804-5.4950.211860.20614650.20615510.9430.9491000.21
5.495-6.6070.255750.23212760.23313510.9330.9381000.234
6.607-8.8720.216680.18310270.18510950.9510.9641000.196
8.872-20.0010.245440.197020.1947470.9520.94799.86610.206

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