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- PDB-9f63: Crystal structure of Saccharomyces cerevisiae pH nine-sensitive p... -

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Basic information

Entry
Database: PDB / ID: 9f63
TitleCrystal structure of Saccharomyces cerevisiae pH nine-sensitive protein 1 (PNS1)
ComponentsProtein PNS1
KeywordsMEMBRANE PROTEIN / Choline transporter-like family / CTL
Function / homologyCholine transporter-like / Plasma-membrane choline transporter / transmembrane transporter activity / cell periphery / transmembrane transport / membrane / plasma membrane / Protein PNS1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsDriller, J.H. / Pedersen, B.P.
Funding support Denmark, European Union, 2items
OrganizationGrant numberCountry
LundbeckfondenR380-2021-1207 Denmark
H2020 Marie Curie Actions of the European Commission890822European Union
CitationJournal: To Be Published
Title: S. cerevisiae pH nine-sensitive protein 1 is not a choline transporter.
Authors: Driller, J.H. / Pedersen, B.P.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PNS1


Theoretical massNumber of molelcules
Total (without water)63,4641
Polymers63,4641
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.449, 91.262, 108.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Protein PNS1 / pH nine-sensitive protein 1


Mass: 63463.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PNS1, YOR161C, O3568 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12412
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 292 K / Method: lipidic cubic phase
Details: 0.1M (NH4)2PO4, 0.1M HEPES 7.0, 32% PEG 400, 6mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9764 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.73→48.47 Å / Num. obs: 18374 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 81.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.057 / Rrim(I) all: 0.145 / Χ2: 1 / Net I/σ(I): 8.8 / Num. measured all: 118497
Reflection shellResolution: 2.73→2.86 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 2.212 / Num. measured all: 16041 / Num. unique obs: 2397 / CC1/2: 0.413 / Rpim(I) all: 0.922 / Rrim(I) all: 2.399 / Χ2: 1 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
PHASER1.18.2_3874phasing
RefinementMethod to determine structure: SAD / Resolution: 2.73→29.29 Å / SU ML: 0.4165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2846 918 5.01 %
Rwork0.2322 17396 -
obs0.2348 18314 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.2 Å2
Refinement stepCycle: LAST / Resolution: 2.73→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 0 12 3381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663467
X-RAY DIFFRACTIONf_angle_d0.85214703
X-RAY DIFFRACTIONf_chiral_restr0.0469528
X-RAY DIFFRACTIONf_plane_restr0.007566
X-RAY DIFFRACTIONf_dihedral_angle_d23.9495458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.880.36581280.3112429X-RAY DIFFRACTION99.53
2.88-3.060.37111290.30052454X-RAY DIFFRACTION99.92
3.06-3.290.31891290.25692436X-RAY DIFFRACTION100
3.29-3.620.30181300.24992470X-RAY DIFFRACTION99.96
3.62-4.140.28551300.22082479X-RAY DIFFRACTION99.96
4.14-5.220.2851320.22182507X-RAY DIFFRACTION99.92
5.22-29.290.24991400.21612621X-RAY DIFFRACTION99.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.842344683640.05285041543490.2199409699272.692396716381.03514014862.61329147235-0.09616414312940.04454759118130.0762544367848-0.009899363600330.0174157663009-0.2156877992830.02781398885570.3453004868150.07374064315530.5148739102920.003841517329680.02870583508990.5445467032780.04239591684380.500927168052-21.345063342527.1608279983-21.4443089556
25.71832428124-4.58903719611-3.096280067351.999985188344.405597517412.000041315960.06017219970290.1281092727250.148626383821-0.8578430080580.4152927828221.52291475961-0.5874465043-1.89055143995-0.4675213469681.16983844760.0528258673073-0.03311465021791.123039872140.0544880131851.203352876575.3471190907620.8104118343-57.1164887124
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain 'A' and resid 128 through 537)128 - 53740 - 422
22(chain 'A' and resid 110 through 115 )110 - 11534 - 39

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