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- PDB-5y78: Crystal structure of the triose-phosphate/phosphate translocator ... -

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Basic information

Entry
Database: PDB / ID: 5y78
TitleCrystal structure of the triose-phosphate/phosphate translocator in complex with inorganic phosphate
ComponentsPutative hexose phosphate translocator
KeywordsTRANSPORT PROTEIN / Chloroplast / inner envelop membrane / antiporter / sugar phosphate
Function / homologySugar phosphate transporter domain / Triose-phosphate Transporter family / : / antiporter activity / Golgi apparatus / membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Putative hexose phosphate translocator
Function and homology information
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, Y. / Nishizawa, T. / Takemoto, M. / Kumazaki, K. / Yamashita, K. / Hirata, K. / Minoda, A. / Nagatoishi, S. / Tsumoto, K. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Plants / Year: 2017
Title: Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Authors: Lee, Y. / Nishizawa, T. / Takemoto, M. / Kumazaki, K. / Yamashita, K. / Hirata, K. / Minoda, A. / Nagatoishi, S. / Tsumoto, K. / Ishitani, R. / Nureki, O.
History
DepositionAug 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hexose phosphate translocator
B: Putative hexose phosphate translocator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,31546
Polymers73,1502
Non-polymers15,16544
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-44 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.550, 164.970, 41.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative hexose phosphate translocator / Sugar-phosphate:phosphate translocator / DMT family


Mass: 36575.195 Da / Num. of mol.: 2 / Fragment: UNP residues 91-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: Gasu_48050, Gs48050.1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B5AJT1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG200, MES, (NH4)2HPO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL32XU11
SYNCHROTRONSPring-8 BL32XU21
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDDec 16, 2015
DECTRIS EIGER X 9M2PIXELOct 16, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 2.1→50 Å / Num. obs: 43639 / % possible obs: 99.8 % / Redundancy: 90.3 % / CC1/2: 0.995 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 87 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.653 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I20

5i20


Resolution: 2.1→48.866 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.07
RfactorNum. reflection% reflection
Rfree0.2256 2177 4.99 %
Rwork0.1947 --
obs0.1963 43607 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 568 283 5572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025383
X-RAY DIFFRACTIONf_angle_d0.5057149
X-RAY DIFFRACTIONf_dihedral_angle_d16.5113161
X-RAY DIFFRACTIONf_chiral_restr0.037812
X-RAY DIFFRACTIONf_plane_restr0.004832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.14560.29741340.27122554X-RAY DIFFRACTION100
2.1456-2.19550.30231400.25992571X-RAY DIFFRACTION100
2.1955-2.25040.2721280.25022528X-RAY DIFFRACTION100
2.2504-2.31130.30771380.24542571X-RAY DIFFRACTION100
2.3113-2.37930.25251310.22252534X-RAY DIFFRACTION100
2.3793-2.45610.24691370.20322582X-RAY DIFFRACTION100
2.4561-2.54390.23051310.19072553X-RAY DIFFRACTION100
2.5439-2.64570.2161340.18242571X-RAY DIFFRACTION100
2.6457-2.76610.20271390.17292582X-RAY DIFFRACTION100
2.7661-2.91190.19471360.16912550X-RAY DIFFRACTION100
2.9119-3.09430.23921360.17872602X-RAY DIFFRACTION100
3.0943-3.33320.23041340.18072599X-RAY DIFFRACTION100
3.3332-3.66850.22141390.17572600X-RAY DIFFRACTION100
3.6685-4.19910.17771400.1742643X-RAY DIFFRACTION100
4.1991-5.28940.20711330.18032594X-RAY DIFFRACTION97
5.2894-48.87910.21731470.20732796X-RAY DIFFRACTION100

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