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- PDB-8oyf: Crystal structure of ASBTNM in lipidic cubic phase without substr... -

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Basic information

Entry
Database: PDB / ID: 8oyf
TitleCrystal structure of ASBTNM in lipidic cubic phase without substrate bound
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / Secondary Membrane Transporter
Function / homologyBile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / NICKEL (II) ION / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATIDYLETHANOLAMINE / Transporter
Function and homology information
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBecker, P. / Cameron, A.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118772 United States
CitationJournal: Biorxiv / Year: 2023
Title: Mechanism of substrate binding and transport in BASS transporters.
Authors: Becker, P. / Naughton, F.B. / Brotherton, D.H. / Pacheco-Gomez, R. / Beckstein, O. / Cameron, A.D.
History
DepositionMay 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,93710
Polymers33,8371
Non-polymers2,1009
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-35 kcal/mol
Surface area13950 Å2
Unit cell
Length a, b, c (Å)49.479, 80.609, 86.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transporter


Mass: 33836.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: NMB0705 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K0A9

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Non-polymers , 6 types, 43 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 0.1M Sodium Chloride, 0.1M Hepes pH 7.0, 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→59 Å / Num. obs: 20744 / % possible obs: 99.37 % / Redundancy: 7.1 % / Biso Wilson estimate: 30.01 Å2 / CC1/2: 0.957 / CC star: 0.989 / Rmerge(I) obs: 0.1356 / Rpim(I) all: 0.05402 / Rrim(I) all: 0.1467 / Net I/σ(I): 6.68
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.8541 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 14741 / CC1/2: 0.658 / CC star: 0.891 / Rpim(I) all: 0.3315 / Rrim(I) all: 0.9198 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→58.96 Å / SU ML: 0.2151 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2387 1089 5.2 %
Rwork0.2114 36288 -
obs0.2129 20691 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 96 34 2409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232425
X-RAY DIFFRACTIONf_angle_d0.52833289
X-RAY DIFFRACTIONf_chiral_restr0.0368401
X-RAY DIFFRACTIONf_plane_restr0.0038387
X-RAY DIFFRACTIONf_dihedral_angle_d13.4948859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26781180.30652637X-RAY DIFFRACTION98.32
2.15-2.210.33071460.27132582X-RAY DIFFRACTION98.88
2.21-2.280.27731310.26582579X-RAY DIFFRACTION97.76
2.28-2.350.26521310.22512618X-RAY DIFFRACTION98.32
2.35-2.430.21081350.20542621X-RAY DIFFRACTION98.89
2.43-2.530.22941440.20022582X-RAY DIFFRACTION98.63
2.53-2.650.20021340.18582602X-RAY DIFFRACTION98.28
2.65-2.790.23681510.19942611X-RAY DIFFRACTION98.12
2.79-2.960.20351530.19762584X-RAY DIFFRACTION98.45
2.96-3.190.1861490.19282574X-RAY DIFFRACTION98.2
3.19-3.510.25031600.20332563X-RAY DIFFRACTION97.56
3.51-4.020.21831380.1932591X-RAY DIFFRACTION98.34
4.02-5.060.23111330.20562614X-RAY DIFFRACTION98.49
5.06-58.960.27241660.22272530X-RAY DIFFRACTION96.7
Refinement TLS params.Method: refined / Origin x: 3.36249657173 Å / Origin y: -9.71381233022 Å / Origin z: -19.890386443 Å
111213212223313233
T0.256486970534 Å2-0.00730616469762 Å20.0306351108875 Å2-0.25573464443 Å20.00777674553478 Å2--0.274267861804 Å2
L1.39070789269 °20.0161762954391 °20.112145942324 °2-2.22916753671 °2-0.326503785943 °2--2.39840032999 °2
S-0.023844821948 Å °-0.000696523479398 Å °-0.0952791367287 Å °0.021140155502 Å °0.0385183947121 Å °0.0790663568201 Å °0.101828987344 Å °-0.0802813528478 Å °0.00142457863668 Å °
Refinement TLS groupSelection details: all

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