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- PDB-5a9i: Crystal structure of the extracellular domain of PepT2 -

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Basic information

Entry
Database: PDB / ID: 5a9i
TitleCrystal structure of the extracellular domain of PepT2
ComponentsSOLUTE CARRIER FAMILY 15 MEMBER 2
KeywordsTRANSPORT PROTEIN / PEPT2 / EXTRACELLULAR DOMAIN / MFS
Function / homology
Function and homology information


high-affinity oligopeptide transmembrane transporter activity / tripeptide import across plasma membrane / oligopeptide transport / dipeptide transport / peptidoglycan transport / dipeptide import across plasma membrane / tripeptide transmembrane transporter activity / metanephric proximal tubule development / peptide:proton symporter activity / antibacterial innate immune response ...high-affinity oligopeptide transmembrane transporter activity / tripeptide import across plasma membrane / oligopeptide transport / dipeptide transport / peptidoglycan transport / dipeptide import across plasma membrane / tripeptide transmembrane transporter activity / metanephric proximal tubule development / peptide:proton symporter activity / antibacterial innate immune response / dipeptide transmembrane transporter activity / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / xenobiotic transport / renal absorption / phagocytic vesicle membrane / protein transport / 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 / Alpha/beta knot methyltransferases / MFS transporter superfamily
Similarity search - Domain/homology
CITRIC ACID / Solute carrier family 15 member 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.84 Å
AuthorsBeale, J.H. / 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 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_CC_half / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOLUTE CARRIER FAMILY 15 MEMBER 2
B: SOLUTE CARRIER FAMILY 15 MEMBER 2
C: SOLUTE CARRIER FAMILY 15 MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5616
Polymers65,0853
Non-polymers4763
Water1,67593
1
A: SOLUTE CARRIER FAMILY 15 MEMBER 2


Theoretical massNumber of molelcules
Total (without water)21,6951
Polymers21,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SOLUTE CARRIER FAMILY 15 MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1714
Polymers21,6951
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SOLUTE CARRIER FAMILY 15 MEMBER 2


Theoretical massNumber of molelcules
Total (without water)21,6951
Polymers21,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.750, 95.750, 165.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.70812, -0.58968, 0.38839), (-0.59794, -0.79334, -0.11433), (0.37555, -0.15128, -0.91437)-31.15241, 121.04666, 327.13208
2given(0.90784, -0.29069, -0.3022), (0.18368, -0.3722, 0.9098), (-0.37695, -0.88146, -0.2845)100.91999, -103.9085, 284.10938

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Components

#1: Protein SOLUTE CARRIER FAMILY 15 MEMBER 2 / PEPT2 / KIDNEY H(+)/PEPTIDE COTRANSPORTER / OLIGOPEPTIDE TRANSPORTER / KIDNEY ISOFORM / PEPTIDE TRANSPORTER 2


Mass: 21694.936 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 410-601
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PLOU3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63424
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCITRATE (CIT): FROM CRYSTALLISATION CONDITION

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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: 3.47 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)3 CITRATE PH 5.8, 21 % PEG 3350. 10 MG.ML AT 20 DEGREES CELCIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.81→58 Å / Num. obs: 21317 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 14 % / Biso Wilson estimate: 86.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.7
Reflection shellResolution: 2.81→2.96 Å / Redundancy: 10 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.697 / % possible all: 69.7

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.84→47.87 Å / Cor.coef. Fo:Fc: 0.9371 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.733 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.76 / SU Rfree Blow DPI: 0.324 / SU Rfree Cruickshank DPI: 0.328
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1090 5.11 %RANDOM
Rwork0.1928 ---
obs0.1954 21317 99.65 %-
Displacement parametersBiso mean: 75.13 Å2
Baniso -1Baniso -2Baniso -3
1--4.1653 Å20 Å20 Å2
2---4.1653 Å20 Å2
3---8.3307 Å2
Refine analyzeLuzzati coordinate error obs: 0.465 Å
Refinement stepCycle: LAST / Resolution: 2.84→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 32 93 4670
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014664HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.296319HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1631SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes129HARMONIC2
X-RAY DIFFRACTIONt_gen_planes671HARMONIC5
X-RAY DIFFRACTIONt_it4664HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion22.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion616SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4916SEMIHARMONIC4
LS refinement shellResolution: 2.84→2.98 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3104 130 4.78 %
Rwork0.2394 2592 -
all0.2426 2722 -
obs--99.65 %
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)
14.72460.6688-0.64697.20661.43762.7721-0.2640.24670.1821-0.59410.22260.5945-0.3924-0.40880.04140.0561-0.0799-0.1139-0.20260.0308-0.1622-14.243173.9555167.598
21.7297-0.3483-0.17283.25031.21535.98850.0435-0.05680.05170.04450.04350.229-0.1992-0.7435-0.0870.05010.0374-0.0528-0.0556-0.0526-0.1271-16.478461.6678187.366
34.02020.7028-0.03395.09191.08316.61620.16830.17940.18760.2801-0.12450.1490.1695-0.5306-0.0438-0.0364-0.21280.0611-0.1417-0.0635-0.2322-19.760152.0021157.135
41.3970.5931-1.28124.2071.21236.22710.3293-0.01550.6055-0.1933-0.1189-0.0557-0.4992-0.1937-0.2103-0.0867-0.15460.1223-0.0599-0.0216-0.1023-6.416360.4251140.509
56.71040.20240.73035.50510.87613.10470.2926-0.094-0.224-0.3788-0.36240.49910.3525-0.41880.06980.28360.1872-0.1132-0.2836-0.1079-0.30415.56518.5843176.472
64.9017-2.58440.5096.46923.65456.7370.020.2965-0.4415-0.2031-0.1628-0.32380.07810.07650.1427-0.15090.1448-0.0556-0.1877-0.20760.146911.822840.5059182.725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|410 - A|504 }
2X-RAY DIFFRACTION2{ A|514 - A|601 }
3X-RAY DIFFRACTION3{ B|410 - B|504 }
4X-RAY DIFFRACTION4{ B|514 - B|601 }
5X-RAY DIFFRACTION5{ C|410 - C|504 }
6X-RAY DIFFRACTION6{ C|514 - C|601 }

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