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- PDB-5d58: In meso in situ serial X-ray crystallography structure of the Pep... -

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Basic information

Entry
Database: PDB / ID: 5d58
TitleIn meso in situ serial X-ray crystallography structure of the PepTSt-Ala-Phe complex at 100 K
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN
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
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / ALANINE / PHENYLALANINE / PHOSPHATE ION / Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuang, C.-Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 10, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,53227
Polymers52,7821
Non-polymers7,75026
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-1 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.160, 109.520, 111.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / PepTst


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)
Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8

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Non-polymers , 6 types, 90 molecules

#2: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 314.460 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C18H34O4
#6: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 250-325 mM NH4H2PO4, 100 mM HEPES, pH 7.0, 21-22 %(v/v) PEG 400 and 10 mM Ala-Phe
PH range: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24159 / % possible obs: 99.4 % / Redundancy: 4.3 % / Net I/σ(I): 9.31
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.18 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4d2c

4d2c


Resolution: 2.4→45.682 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 1218 5.04 %
Rwork0.2091 --
obs0.2113 24159 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 485 64 4041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054058
X-RAY DIFFRACTIONf_angle_d0.9325385
X-RAY DIFFRACTIONf_dihedral_angle_d18.9111491
X-RAY DIFFRACTIONf_chiral_restr0.033586
X-RAY DIFFRACTIONf_plane_restr0.005631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.3081330.26552511X-RAY DIFFRACTION99
2.4961-2.60970.28261500.25072492X-RAY DIFFRACTION100
2.6097-2.74730.3111120.2522549X-RAY DIFFRACTION100
2.7473-2.91940.32051230.23882504X-RAY DIFFRACTION98
2.9194-3.14470.32671310.24612534X-RAY DIFFRACTION99
3.1447-3.46110.2691490.23812528X-RAY DIFFRACTION100
3.4611-3.96170.25591350.19322572X-RAY DIFFRACTION100
3.9617-4.99030.22041480.17282582X-RAY DIFFRACTION100
4.9903-45.68980.20431370.19652669X-RAY DIFFRACTION99

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