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- PDB-4xnj: X-ray structure of PepTst2 -

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Basic information

Entry
Database: PDB / ID: 4xnj
TitleX-ray structure of PepTst2
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / 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 / Growth Hormone; Chain: A; / Major facilitator superfamily domain ...: / 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 / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / PHOSPHATE ION / Di-/tripeptide transporter
Similarity search - Component
Biological speciesStreptococcus thermophilus LMG 18311 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuang, C.Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M.
Funding support Ireland, United States, 2items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
National Institutes of HealthGM75915, P50GM073210, U54GM094599 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Panepucci, E. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 10, 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)56,96515
Polymers52,7821
Non-polymers4,18314
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-5 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.880, 110.160, 110.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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Components

#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 LMG 18311 (bacteria)
Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8
#2: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 250-350 mM NH4H2PO4, 100 mM HEPES, pH7.0, 21-22% pEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 28208 / % possible obs: 99.2 % / Redundancy: 4.4 % / Net I/σ(I): 9.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.3 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2B

4d2b


Resolution: 2.3→49.336 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1294 4.59 %
Rwork0.2028 --
obs0.2051 28208 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 291 53 3957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073998
X-RAY DIFFRACTIONf_angle_d1.1825368
X-RAY DIFFRACTIONf_dihedral_angle_d17.0941432
X-RAY DIFFRACTIONf_chiral_restr0.043601
X-RAY DIFFRACTIONf_plane_restr0.006638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.2991380.28192936X-RAY DIFFRACTION99
2.3921-2.5010.27721280.25742962X-RAY DIFFRACTION100
2.501-2.63280.29111350.23062979X-RAY DIFFRACTION100
2.6328-2.79780.29071660.23082952X-RAY DIFFRACTION100
2.7978-3.01380.25561230.22022983X-RAY DIFFRACTION99
3.0138-3.3170.26941670.21612956X-RAY DIFFRACTION100
3.317-3.79680.26591290.19723013X-RAY DIFFRACTION99
3.7968-4.7830.23571540.17983021X-RAY DIFFRACTION100
4.783-49.34730.21941540.18393112X-RAY DIFFRACTION99

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