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- PDB-6yog: Structure of PepTSt from COC IMISX setup collected by still seria... -

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Basic information

Entry
Database: PDB / ID: 6yog
TitleStructure of PepTSt from COC IMISX setup collected by still serial crystallography on crystals prelocated by 2D X-ray phase-contrast imaging
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / 2D X-ray phase-contrast imaging / IMISX / in situ rotation images / prelocation / still images / serial crystallography / HYDROLASE
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane
Similarity search - Function
Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / TRIETHYLENE GLYCOL / PHOSPHATE ION / Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuang, C.-Y. / Martiel, I. / Villanueva-Perez, P. / Panepucci, E. / Caffrey, M. / Wang, M.
CitationJournal: Iucrj / Year: 2020
Title: Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography.
Authors: Martiel, I. / Huang, C.Y. / Villanueva-Perez, P. / Panepucci, E. / Basu, S. / Caffrey, M. / Pedrini, B. / Bunk, O. / Stampanoni, M. / Wang, M.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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: Di-or tripeptide:H+ symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,43724
Polymers52,7821
Non-polymers6,65423
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint4 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.430, 110.700, 111.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Di-or tripeptide:H+ symporter


Mass: 52782.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria)
Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8

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Non-polymers , 5 types, 100 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C18H34O4
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 250-325 mM NH4H2PO4, 100 mM HEPES, pH 7.0, 21-22 %(v/v) PEG 400 and 10 mM Ala-Phe

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→55.64 Å / Num. obs: 28437 / % possible obs: 100 % / Redundancy: 51.9 % / CC1/2: 0.92 / Rrim(I) all: 0.17 / Net I/σ(I): 3.73
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 32.6 % / Num. unique obs: 2806 / CC1/2: 0.33 / Rrim(I) all: 2.15 / % possible all: 99.95
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: IMISX / Sample dehydration prevention: COC sandwich / Sample holding: IMISX / Support base: 3D-printed holder in standard goniometer base

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Processing

Software
NameVersionClassification
CrystFELdata scaling
PHENIXdev_3311refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D58

5d58


Resolution: 2.3→55.64 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.03
RfactorNum. reflection% reflection
Rfree0.2723 1422 5 %
Rwork0.2412 --
obs0.2428 28436 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.69 Å2 / Biso mean: 58.2949 Å2 / Biso min: 27.05 Å2
Refinement stepCycle: final / Resolution: 2.3→55.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 463 77 4015
Biso mean--69.43 49.34 -
Num. residues----448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.38220.35151400.28852666
2.3822-2.47760.29521400.27752658
2.4776-2.59040.29651410.25672676
2.5904-2.72690.25511400.23722664
2.7269-2.89780.25571420.23592692
2.8978-3.12150.28321410.22942686
3.1215-3.43560.28331420.23452698
3.4356-3.93260.2741420.2392695
3.9326-4.95420.24951440.22752737
4.9542-55.640.27611500.25042842

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