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- PDB-6oh4: X-ray crystal structure of the mouse CMP-sialic acid transporter ... -

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Basic information

Entry
Database: PDB / ID: 6oh4
TitleX-ray crystal structure of the mouse CMP-sialic acid transporter in complex with CMP, by hanging drop vapor diffusion
ComponentsCMP-sialic acid transporter
KeywordsTRANSPORT PROTEIN / drug/metabolite transporter / nucleotide-sugar / sialic acid / glycosylation
Function / homology
Function and homology information


CMP-N-acetylneuraminate transmembrane transporter activity / UDP-galactose transmembrane transporter activity / CMP-N-acetylneuraminate transmembrane transport / Transport of nucleotide sugars / Sialic acid metabolism / antiporter activity / integral component of Golgi membrane / carbohydrate transport / integral component of membrane
Similarity search - Function
Nucleotide-sugar transporter / Nucleotide-sugar transporter
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / CMP-sialic acid transporter
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.38 Å
AuthorsAhuja, S. / Whorton, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130909 United States
CitationJournal: Elife / Year: 2019
Title: Structural basis for mammalian nucleotide sugar transport.
Authors: Ahuja, S. / Whorton, M.R.
History
DepositionApr 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMP-sialic acid transporter
B: CMP-sialic acid transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6364
Polymers74,9902
Non-polymers6462
Water0
1
A: CMP-sialic acid transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8182
Polymers37,4951
Non-polymers3231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CMP-sialic acid transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8182
Polymers37,4951
Non-polymers3231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)51.820, 193.960, 66.440
Angle α, β, γ (deg.)90.00, 101.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 317
2010B15 - 317
DetailsThe authors state that there are no biologically relevant macromolecular assemblies in this structure.

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Components

#1: Protein CMP-sialic acid transporter / / CMP-Sia-Tr / Solute carrier family 35 member A1


Mass: 37494.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc35a1 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: Q61420
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION

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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: 4.36 Å3/Da / Density % sol: 71.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25.6-26.8% PEG 400, 0.1 M Tris pH 8.5, and 0.1 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03313 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03313 Å / Relative weight: 1
ReflectionResolution: 3.38→49 Å / Num. obs: 11456 / % possible obs: 67.3 % / Redundancy: 3.6 % / Net I/σ(I): 6.7
Reflection shellResolution: 3.38→3.5 Å / Num. unique obs: 51

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.38→49 Å / Cor.coef. Fo:Fc: 0.761 / Cor.coef. Fo:Fc free: 0.691 / SU B: 53.451 / SU ML: 0.765 / Cross valid method: THROUGHOUT / ESU R Free: 0.79 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32106 573 4.8 %RANDOM
Rwork0.28942 ---
obs0.29094 11456 67.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 143.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å20.84 Å2
2---1.5 Å2-0 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 3.38→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 42 0 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024590
X-RAY DIFFRACTIONr_bond_other_d0.0010.024465
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.9866271
X-RAY DIFFRACTIONr_angle_other_deg0.83310243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62722.913127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64515722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.3881510
X-RAY DIFFRACTIONr_chiral_restr0.0450.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02958
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_it3.55914.8572388
X-RAY DIFFRACTIONr_mcbond_other3.55914.8562387
X-RAY DIFFRACTIONr_mcangle_it6.06422.272978
X-RAY DIFFRACTIONr_mcangle_other6.06322.2712979
X-RAY DIFFRACTIONr_scbond_it3.10514.9692202
X-RAY DIFFRACTIONr_scbond_other3.10314.9722198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.60722.4213288
X-RAY DIFFRACTIONr_long_range_B_refined9.4925230
X-RAY DIFFRACTIONr_long_range_B_other9.4935231
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19128 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.384→3.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.14 2 -
Rwork0.335 51 -
obs--3.93 %

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