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- PDB-5y79: Crystal structure of the triose-phosphate/phosphate translocator ... -

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Basic information

Entry
Database: PDB / ID: 5y79
TitleCrystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate
ComponentsPutative hexose phosphate translocator
KeywordsTRANSPORT PROTEIN / Chloroplast / inner envelop membrane / antiporter / sugar phosphate
Function / homologySugar phosphate transporter domain / Triose-phosphate Transporter family / : / membrane / 3-PHOSPHOGLYCERIC ACID / CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Putative hexose phosphate translocator
Function and homology information
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)85,12137
Polymers73,1502
Non-polymers11,97035
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-37 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.050, 165.330, 41.140
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-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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, Na-citrate, 3K-citrate, 2Na(3-PGA)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38123 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 0.994 / Net I/σ(I): 13.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 27 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.698 / % possible all: 99.9

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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: 2.2→48.998 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.2292 1991 5.23 %
Rwork0.1906 --
obs0.1926 38071 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 461 222 5396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035279
X-RAY DIFFRACTIONf_angle_d0.6377057
X-RAY DIFFRACTIONf_dihedral_angle_d18.1283067
X-RAY DIFFRACTIONf_chiral_restr0.04816
X-RAY DIFFRACTIONf_plane_restr0.004828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1999-2.2550.32551360.29272542X-RAY DIFFRACTION100
2.255-2.31590.33231410.26212533X-RAY DIFFRACTION100
2.3159-2.38410.29481390.22792512X-RAY DIFFRACTION100
2.3841-2.4610.23551420.21422548X-RAY DIFFRACTION100
2.461-2.5490.23911410.19762567X-RAY DIFFRACTION100
2.549-2.6510.25621400.18082517X-RAY DIFFRACTION100
2.651-2.77170.21651410.1672554X-RAY DIFFRACTION100
2.7717-2.91780.21711430.16882573X-RAY DIFFRACTION100
2.9178-3.10060.22121410.17172551X-RAY DIFFRACTION100
3.1006-3.33990.20971430.18362573X-RAY DIFFRACTION100
3.3399-3.67590.21271430.17622584X-RAY DIFFRACTION100
3.6759-4.20760.24011440.17412617X-RAY DIFFRACTION100
4.2076-5.30010.20041450.17412626X-RAY DIFFRACTION99
5.3001-49.01040.20441520.20442783X-RAY DIFFRACTION100

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