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- PDB-5a9d: Crystal structure of the extracellular domain of PepT1 -

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Basic information

Entry
Database: PDB / ID: 5a9d
TitleCrystal structure of the extracellular domain of PepT1
ComponentsSOLUTE CARRIER FAMILY 15 MEMBER 1
KeywordsTRANSPORT PROTEIN / PEPT1 / EXTRACELLULAR CELLULAR DOMAIN / IGG-LIKE FOLD
Function / homology
Function and homology information


negative regulation of amino acid transport / Proton/oligopeptide cotransporters / proton-dependent oligopeptide secondary active transmembrane transporter activity / channel inhibitor activity / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity / dipeptide transmembrane transporter activity / plasma membrane => GO:0005886 / brush border ...negative regulation of amino acid transport / Proton/oligopeptide cotransporters / proton-dependent oligopeptide secondary active transmembrane transporter activity / channel inhibitor activity / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity / dipeptide transmembrane transporter activity / plasma membrane => GO:0005886 / brush border / protein transport / membrane => GO:0016020 / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Oligopeptide transporter / 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 / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 15 member 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBeale, J.H. / Bird, L.E. / Owens, R.J. / Newstead, S.
CitationJournal: Structure / Year: 2015
Title: Crystal Structures of the Extracellular Domain from Pept1 and Pept2 Provide Novel Insights Into Mammalian Peptide Transport
Authors: Beale, J.H. / Parker, J.L. / Samsudin, F. / Barrett, A.L. / Senan, A. / Bird, L.E. / Scott, D. / Owens, R.J. / Sanson, M.S.P. / Tucker, S.J. / Meredith, D. / Fowler, P.W. / Newstead, S.
History
DepositionJul 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SOLUTE CARRIER FAMILY 15 MEMBER 1
B: SOLUTE CARRIER FAMILY 15 MEMBER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0175
Polymers41,7402
Non-polymers2763
Water2,702150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-10.9 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.480, 70.330, 111.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99902, -0.0423, -0.01325), (-0.04433, 0.95115, 0.30554), (-0.00032, 0.30583, -0.95209)
Vector: -23.01291, 3.4792, -26.23655)

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Components

#1: Protein SOLUTE CARRIER FAMILY 15 MEMBER 1 / INTESTINAL H(+)/PEPTIDE COTRANSPORTER / OLIGOPEPTIDE TRANSPORTER / SMALL INTESTINE ISOFORM / ...INTESTINAL H(+)/PEPTIDE COTRANSPORTER / OLIGOPEPTIDE TRANSPORTER / SMALL INTESTINE ISOFORM / PEPTIDE TRANSPORTER 1 / PROTON- COUPLED DIPEPTIDE COTRANSPORTER / EXTRACELLULAR DOMAIN


Mass: 20870.225 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 391-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: POPINM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JIP7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 6000, 0.1 M MES PH 6.0, 0.2 M AMMONIUM CHLORIDE, AT 10 MG.ML-1 AND A 4 DEGREES CELCIUS USING SITTING DROP VAPOUR DIFFUSION PLATES.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.1→43 Å / Num. obs: 25179 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 43.84 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.7 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.62 Å / Cor.coef. Fo:Fc: 0.9437 / Cor.coef. Fo:Fc free: 0.9252 / SU R Cruickshank DPI: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1290 5.17 %RANDOM
Rwork0.1947 ---
obs0.1969 24975 99.19 %-
Displacement parametersBiso mean: 57.39 Å2
Baniso -1Baniso -2Baniso -3
1--5.0644 Å20 Å20 Å2
2---3.3458 Å20 Å2
3---8.4102 Å2
Refine analyzeLuzzati coordinate error obs: 0.322 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 18 150 3098
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184161HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1051SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes445HARMONIC5
X-RAY DIFFRACTIONt_it3061HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion17.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion414SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3461SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.269 152 5.56 %
Rwork0.2223 2581 -
all0.2249 2733 -
obs--99.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8275-0.13252.7710.88730.21648.3154-0.1384-0.03970.37430.1823-0.04080.0883-0.3963-0.24430.1792-0.0562-0.0241-0.0308-0.09920.0236-0.0966-14.30950.26063.8807
22.3133-0.35761.00264.5882-2.35645.00720.0251-0.1233-0.0031-0.35890.20320.15080.3035-0.2095-0.2284-0.0336-0.04690.0061-0.15270.0059-0.1472-27.3765-2.1568-22.7808
35.0943-1.16461.65830.96290.15913.93470.1383-0.10630.4718-0.2154-0.0304-0.1191-0.44640.5442-0.1079-0.0624-0.12450.078-0.0366-0.0221-0.1132-8.73785.5732-30.0582
46.86681.2984-0.80562.4888-0.17741.4939-0.07450.2861-0.11140.07220.1013-0.4901-0.15620.5442-0.0268-0.253-0.0994-0.05770.18770.0692-0.27894.9416-3.9948-5.0096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|394 - A|479 }
2X-RAY DIFFRACTION2{ A|485 - A|578 }
3X-RAY DIFFRACTION3{ B|394 - B|479 }
4X-RAY DIFFRACTION4{ B|488 - B|579 }

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