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- PDB-4tpg: Selectivity mechanism of a bacterial homologue of the human drug ... -

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Basic information

Entry
Database: PDB / ID: 4tpg
TitleSelectivity mechanism of a bacterial homologue of the human drug peptide transporters PepT1 and PepT2
Components
  • Ala-L-3-Br-Tyr-Ala
  • Proton:oligopeptide symporter POT family
KeywordsMEMBRANE PROTEIN / complex / secondary active transporter
Function / homology
Function and homology information


dipeptide transmembrane transport / tripeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / identical protein binding / plasma membrane
Similarity search - Function
: / Dipeptide/tripeptide permease / MFS general substrate transporter like domains / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE / Proton:oligopeptide symporter POT family
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.91 Å
AuthorsGuettou, F. / Quistgaard, E.M. / Raba, M. / Moberg, P. / Low, C. / Nordlund, P.
Funding support Sweden, Singapore, 4items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Swedish Cancer Society Sweden
integrated EU project EDICT Sweden
NRF-CRP grant Singapore
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2.
Authors: Guettou, F. / Quistgaard, E.M. / Raba, M. / Moberg, P. / Low, C. / Nordlund, P.
History
DepositionJun 7, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Data collection
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton:oligopeptide symporter POT family
B: Proton:oligopeptide symporter POT family
E: Ala-L-3-Br-Tyr-Ala
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0166
Polymers114,9293
Non-polymers1,0873
Water00
1
A: Proton:oligopeptide symporter POT family
E: Ala-L-3-Br-Tyr-Ala
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2814
Polymers57,7052
Non-polymers5762
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-2 kcal/mol
Surface area19770 Å2
MethodPISA
2
B: Proton:oligopeptide symporter POT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7352
Polymers57,2241
Non-polymers5111
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint1 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.890, 108.090, 206.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proton:oligopeptide symporter POT family / A secondary active peptide transporter in complex with a tripeptide AYA.


Mass: 57224.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: SO_1277 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EHE6
#2: Protein/peptide Ala-L-3-Br-Tyr-Ala


Type: Polypeptide / Class: Transport activator / Mass: 481.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M phosphate citrate, 36% PEG300, 0.12 M ZnCl2 / PH range: 4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.91→4.01 Å / Num. obs: 31871 / % possible obs: 90.6 % / Redundancy: 4.8 % / Net I/σ(I): 7.14
Reflection shellResolution: 3.91→4.01 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.18 / % possible all: 39.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEP

4lep


Resolution: 3.91→4.01 Å / SU ML: 0.55 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 32.8 / Stereochemistry target values: ML
Details: 52.30 percent of collected reflections collected used in refinement. The crystal suffered severe radiation damage and "died" during collection. Authors had to cut the data prior to ...Details: 52.30 percent of collected reflections collected used in refinement. The crystal suffered severe radiation damage and "died" during collection. Authors had to cut the data prior to refinement dues to bad quality. They also used the online anisotropy server (http://services.mbi.ucla.edu/anisoscale/) for data scaling.
RfactorNum. reflection% reflection
Rfree0.2903 843 5.06 %
Rwork0.2607 --
obs0.2622 16668 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.91→4.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6965 0 71 0 7036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037215
X-RAY DIFFRACTIONf_angle_d0.8519835
X-RAY DIFFRACTIONf_dihedral_angle_d14.132472
X-RAY DIFFRACTIONf_chiral_restr0.0291138
X-RAY DIFFRACTIONf_plane_restr0.0041184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.9053-4.14940.35551090.3471197473
4.1494-4.46880.35341480.29752688100
4.4688-4.91670.32111620.25132744100
4.9167-5.62390.26881620.24122711100
5.6239-7.06941322788100
7.06940.25481300.23572920100
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)
10.55090.8414-0.71973.24980.16521.89780.09360.2242-0.2064-0.4091-0.0372-0.2465-0.13040.18510.00630.69120.0929-0.33610.6867-0.0660.709639.9504171.7102231.3058
21.12280.19711.07072.5801-0.71741.42660.1146-0.0593-0.0723-0.42390.0040.38940.1541-0.27070.07080.75280.0741-0.31970.6659-0.03920.714224.7379124.7789237.0942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B
2X-RAY DIFFRACTION2chain A

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