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- PDB-6rw3: The molecular basis for sugar import in malaria parasites. -

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Basic information

Entry
Database: PDB / ID: 6rw3
TitleThe molecular basis for sugar import in malaria parasites.
ComponentsHexose transporter 1
KeywordsMEMBRANE PROTEIN / transporter
Function / homology
Function and homology information


transmembrane transporter activity / plasma membrane
Similarity search - Function
Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-D-glucopyranose / Hexose transporter 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsQureshi, A. / Matsuoka, R. / Brock, J. / Drew, D.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nature / Year: 2020
Title: The molecular basis for sugar import in malaria parasites.
Authors: Qureshi, A.A. / Suades, A. / Matsuoka, R. / Brock, J. / McComas, S.E. / Nji, E. / Orellana, L. / Claesson, M. / Delemotte, L. / Drew, D.
History
DepositionJun 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.pdbx_database_id_PubMed ..._chem_comp.type / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 26, 2020Group: Database references / Structure summary / Category: citation / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.name / _diffrn_radiation_wavelength.wavelength ..._chem_comp.name / _diffrn_radiation_wavelength.wavelength / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.d_res_low
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexose transporter 1
B: Hexose transporter 1
C: Hexose transporter 1
D: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,74312
Polymers223,3024
Non-polymers1,4418
Water00
1
A: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1863
Polymers55,8251
Non-polymers3602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1863
Polymers55,8251
Non-polymers3602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1863
Polymers55,8251
Non-polymers3602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1863
Polymers55,8251
Non-polymers3602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.740, 189.450, 136.890
Angle α, β, γ (deg.)90.000, 96.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hexose transporter 1 / Putative sugar transporter


Mass: 55825.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ht1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O97467
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 4.35 Å3/Da / Density % sol: 71.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: MES, Magnesium Chloride,PEG 300, NG

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11931N
21931N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.971997
SYNCHROTRONESRF ID23-120.971997
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMay 15, 2018
DECTRIS EIGER R 4M2PIXELAug 5, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9719971
21
ReflectionResolution: 3.65→21.85 Å / Num. obs: 41268 / % possible obs: 99.4 % / Redundancy: 12.4 % / Biso Wilson estimate: 169.99 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.285 / Net I/σ(I): 10
Reflection shellResolution: 3.65→3.8 Å / Num. unique obs: 4095 / CC1/2: 0.21 / CC star: 0.57

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
Aimlessdata scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zw9

4zw9


Resolution: 3.65→21.85 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.573
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 2114 5.12 %RANDOM
Rwork0.2726 ---
obs0.2732 41268 99.9 %-
Displacement parametersBiso max: 286.97 Å2 / Biso mean: 230.56 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--47.82 Å20 Å247.2772 Å2
2--33.7833 Å20 Å2
3---14.0367 Å2
Refine analyzeLuzzati coordinate error obs: 0.76 Å
Refinement stepCycle: final / Resolution: 3.65→21.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13908 0 96 0 14004
Biso mean--189.25 --
Num. residues----1753
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4819SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2260HARMONIC5
X-RAY DIFFRACTIONt_it14340HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1968SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12191SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14340HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg19432HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion21.68
LS refinement shellResolution: 3.65→4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2118 31 3.75 %
Rwork0.2058 795 -
all0.206 826 -
obs--97.01 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
117.1522-11.5517.752921.8084-20.960860.6982-0.7192-1.7475-0.13021.78082.29030.19881.5647-1.7713-1.5712-1.0655-0.30180.0573-0.2395-0.4293-0.804210.6863-44.369771.6479
214.9194-14.42969.973447.2789-24.796225.2651-1.13490.70712.6027-1.45060.5821-2.7329-1.5992-0.84120.5528-1.0277-0.29630.5516-0.38210.0101-0.35034.6249-13.299439.9986
39.8812.9672-8.140542.4131-21.366331.07180.0753-1.6418-0.88621.0568-2.4311-1.27320.79042.0942.3558-1.43250.03620.0002-0.71850.0277-0.749242.0012-81.688722.5961
46.30692.577-4.985133.4748-26.109968.0389-0.0591.28810.3113-2.9828-1.5221-0.3107-3.95460.04061.58111.45450.6965-0.5671-0.9549-0.2147-0.762443.3683-52.7058-11.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A22 - 483
2X-RAY DIFFRACTION2{ B|* }B22 - 480
3X-RAY DIFFRACTION3{ C|* }C22 - 483
4X-RAY DIFFRACTION4{ D|* }D22 - 480

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