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- PDB-5mmt: Inward open PepTSt from Streptococcus thermophilus crystallized i... -

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Basic information

Entry
Database: PDB / ID: 5mmt
TitleInward open PepTSt from Streptococcus thermophilus crystallized in space group P3121
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / Integral membrane protein / Major facilitator superfamily transporter (MFS transporter) / POT PTR or PepT family / proton-coupled peptide transporter
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. / MFS general substrate transporter like domains / 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. / Growth Hormone; Chain: A; ...Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / 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. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsQuistgaard, E.M. / Molledo, M.M. / Nordlund, P. / Loew, C.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council621-2013-5905 Sweden
European Communitys Seventh Framework Programme (FP7/2007-2013) under BioStruct-X
CitationJournal: PLoS ONE / Year: 2017
Title: Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121.
Authors: Quistgaard, E.M. / Martinez Molledo, M. / Low, C.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Di-or tripeptide:H+ symporter


Theoretical massNumber of molelcules
Total (without water)53,6481
Polymers53,6481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.190, 80.190, 293.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 53648.074 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.79 % / Description: Rod-shaped crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.05 M HEPES pH 8.0, 30% PEG550 MME, 1.2% Fos-Choline 10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→44.85 Å / Num. obs: 11881 / % possible obs: 74.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 96.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rsym value: 0.08 / Net I/σ(I): 13.67
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 0.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.13 / CC1/2: 0.834 / % possible all: 5.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.4→44.85 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 36.6
Details: The data set used for refinement was truncated and anisotropically scaled using the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/). Cut-off values for truncation: ...Details: The data set used for refinement was truncated and anisotropically scaled using the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/). Cut-off values for truncation: 3.9 A in the a-direction, 3.7 A in the b-direction and 3.4 A in the best diffracting c-direction of the crystal.
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 589 4.96 %Random
Rwork0.2652 ---
obs0.2662 11292 74.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 127.1 Å2
Refinement stepCycle: LAST / Resolution: 3.4→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 0 3283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053377
X-RAY DIFFRACTIONf_angle_d1.1884604
X-RAY DIFFRACTIONf_dihedral_angle_d11.4821132
X-RAY DIFFRACTIONf_chiral_restr0.045538
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.74050.3994340.3201641X-RAY DIFFRACTION17.4
3.7405-4.28130.32161540.27242964X-RAY DIFFRACTION80
4.2813-5.39260.25791950.23343768X-RAY DIFFRACTION99.9
5.3926-44.850.28542060.28023916X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 85.5225 Å / Origin y: -29.2027 Å / Origin z: 25.7457 Å
111213212223313233
T1.3796 Å2-0.6503 Å2-0.3807 Å2-0.5457 Å20.0886 Å2--0.5299 Å2
L5.4879 °21.1137 °21.3581 °2-3.2331 °21.4566 °2--5.2727 °2
S-0.3592 Å °0.6528 Å °-0.0744 Å °-1.3202 Å °0.5745 Å °0.0902 Å °-0.1144 Å °0.0518 Å °-0.0971 Å °
Refinement TLS groupSelection details: chain 'A'

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