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- PDB-4lep: Structural insights into substrate recognition in proton dependen... -

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Basic information

Entry
Database: PDB / ID: 4lep
TitleStructural insights into substrate recognition in proton dependent oligopeptide transporters
ComponentsProton:oligopeptide symporter POT family
Keywordsmembrane protein / tranport protein / MFS superfamily / Peptide transporter
Function / homology
Function and homology information


dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / membrane / identical protein binding
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
N-[(1R)-1-phosphonoethyl]-L-alaninamide / Proton:oligopeptide symporter POT family
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.2 Å
AuthorsGuettou, F. / Quistgaard, E.M. / Tresaugues, L. / Moberg, P. / Jegerschold, C. / Zhu, L. / Jong, A.J. / Nordlund, P. / Low, C.
CitationJournal: Embo Rep. / Year: 2013
Title: Structural insights into substrate recognition in proton-dependent oligopeptide transporters.
Authors: Guettou, F. / Quistgaard, E.M. / Tresaugues, L. / Moberg, P. / Jegerschold, C. / Zhu, L. / Jong, A.J. / Nordlund, P. / Low, C.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Proton:oligopeptide symporter POT family
B: Proton:oligopeptide symporter POT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9065
Polymers114,4482
Non-polymers4583
Water0
1
A: Proton:oligopeptide symporter POT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4863
Polymers57,2241
Non-polymers2622
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proton:oligopeptide symporter POT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4202
Polymers57,2241
Non-polymers1961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-59 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.240, 107.730, 205.510
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


Mass: 57224.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1277 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EHE6
#2: Chemical ChemComp-AFS / N-[(1R)-1-phosphonoethyl]-L-alaninamide / Alafosfalin / Alafosfalin


Mass: 196.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13N2O4P / Comment: antifungal, antibiotic*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 4.14 Å3/Da / Density % sol: 70.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.5
Details: 40% PEG 300, 0.1 M phosphate citrate, 0.12 M ZnCl2, 3% trimethylamine N-oxide dehydrate pH 11, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2012
RadiationMonochromator: Channel cut Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→29.86 Å / Num. all: 319764 / Num. obs: 24514 / % possible obs: 77.5 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Biso Wilson estimate: 82.21 Å2
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 1.221 / Mean I/σ(I) obs: 1.7 / % possible all: 15.9

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
anisotropyserverdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.2→29.86 Å / SU ML: 0.55 / σ(F): 1.7 / σ(I): 1.7 / Phase error: 37.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3248 1250 5.1 %RANDOM
Rwork0.2748 ---
obs0.2773 24500 77.56 %-
all-24677 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6833 0 25 0 6858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127039
X-RAY DIFFRACTIONf_angle_d1.3379585
X-RAY DIFFRACTIONf_dihedral_angle_d15.972329
X-RAY DIFFRACTIONf_chiral_restr0.0871131
X-RAY DIFFRACTIONf_plane_restr0.0081164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2004-3.32840.4095410.3807608X-RAY DIFFRACTION19
3.3284-3.47970.3927760.38051338X-RAY DIFFRACTION41
3.4797-3.66280.39211000.35381989X-RAY DIFFRACTION60
3.6628-3.89190.33631400.31032598X-RAY DIFFRACTION79
3.8919-4.19160.38161650.29773204X-RAY DIFFRACTION96
4.1916-4.6120.29121740.25193300X-RAY DIFFRACTION100
4.612-5.27620.29411890.23283347X-RAY DIFFRACTION100
5.2762-6.63550.30581830.2933354X-RAY DIFFRACTION100
6.6355-29.86310.31721820.25083512X-RAY DIFFRACTION100
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)
11.41460.0658-0.82424.5648-0.21152.68550.12230.09970.0321-0.6367-0.0579-0.53190.09070.5127-0.09490.57410.10170.35460.74680.00550.73916.179437.6323234.573
20.99860.38530.16225.55180.38014.14150.18760.23720.1467-0.8131-0.1188-0.0922-0.1472-0.1259-0.06610.64810.13650.18410.60590.06070.54252.1633-9.6145229.7485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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