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- PDB-7qoa: Structure of CodB, a cytosine transporter in an outward-facing co... -

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Basic information

Entry
Database: PDB / ID: 7qoa
TitleStructure of CodB, a cytosine transporter in an outward-facing conformation
ComponentsCytosine permease
KeywordsTRANSPORT PROTEIN / Membrane Transporter / Cytosine / Sodium
Function / homology
Function and homology information


cytosine transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function
Cytosine permease / Hydantoin permease / Hydantoin permease / Purine-cytosine permease / Permease for cytosine/purines, uracil, thiamine, allantoin / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 6-AMINOPYRIMIDIN-2(1H)-ONE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Cytosine permease
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHatton, C.E. / Cameron, A.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Embo J. / Year: 2022
Title: Structure of cytosine transport protein CodB provides insight into nucleobase-cation symporter 1 mechanism.
Authors: Hatton, C.E. / Brotherton, D.H. / Spencer, M. / Cameron, A.D.
History
DepositionDec 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosine permease
B: Cytosine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,63713
Polymers88,3842
Non-polymers3,25311
Water1,18966
1
A: Cytosine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2427
Polymers44,1921
Non-polymers2,0506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3956
Polymers44,1921
Non-polymers1,2045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.246, 209.027, 102.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Cytosine permease


Mass: 44191.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: EKQ45_12260 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A857SHB2
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 76 molecules

#2: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-A6L / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / monoolein


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 0.1 M Sodium Cacodylate pH 6.5, 0.45 M NaCl, 39% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.4→73.16 Å / Num. obs: 45754 / % possible obs: 99.41 % / Redundancy: 12.7 % / Biso Wilson estimate: 42.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.3739 / Net I/σ(I): 11.57
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 4436 / CC1/2: 0.466

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JLN

2jln


Resolution: 2.4→73.16 Å / SU ML: 0.331 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2652 2209 4.86 %
Rwork0.2179 43279 -
obs0.2201 45488 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→73.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5883 0 134 66 6083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746144
X-RAY DIFFRACTIONf_angle_d0.90388357
X-RAY DIFFRACTIONf_chiral_restr0.0491019
X-RAY DIFFRACTIONf_plane_restr0.00671013
X-RAY DIFFRACTIONf_dihedral_angle_d13.2955897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.34871390.29252604X-RAY DIFFRACTION98.14
2.45-2.510.34071350.27612675X-RAY DIFFRACTION99.47
2.51-2.570.31861420.25332694X-RAY DIFFRACTION99.47
2.57-2.640.31751230.24812664X-RAY DIFFRACTION99.46
2.64-2.720.28661390.23872682X-RAY DIFFRACTION99.61
2.72-2.810.31571360.22862680X-RAY DIFFRACTION99.54
2.81-2.910.25391340.22172682X-RAY DIFFRACTION99.58
2.91-3.020.30451320.23552721X-RAY DIFFRACTION99.55
3.02-3.160.30651450.25152679X-RAY DIFFRACTION99.82
3.16-3.330.26541390.22552708X-RAY DIFFRACTION99.55
3.33-3.540.27231300.20242714X-RAY DIFFRACTION99.58
3.54-3.810.21261550.1932685X-RAY DIFFRACTION99.16
3.81-4.190.25991460.19692716X-RAY DIFFRACTION99.76
4.19-4.80.24031460.21112725X-RAY DIFFRACTION99.69
4.8-6.050.27861170.22672800X-RAY DIFFRACTION99.59
6.05-73.160.23451510.19652850X-RAY DIFFRACTION98.75

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