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Open data
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Basic information
Entry | Database: PDB / ID: 5a9i | ||||||
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Title | Crystal structure of the extracellular domain of PepT2 | ||||||
![]() | SOLUTE CARRIER FAMILY 15 MEMBER 2 | ||||||
![]() | TRANSPORT PROTEIN / PEPT2 / EXTRACELLULAR DOMAIN / MFS | ||||||
Function / homology | ![]() high-affinity oligopeptide transmembrane transporter activity / Proton/oligopeptide cotransporters / tripeptide import across plasma membrane / peptidoglycan transport / tripeptide transmembrane transporter activity / dipeptide transport / metanephric proximal tubule development / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity ...high-affinity oligopeptide transmembrane transporter activity / Proton/oligopeptide cotransporters / tripeptide import across plasma membrane / peptidoglycan transport / tripeptide transmembrane transporter activity / dipeptide transport / metanephric proximal tubule development / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity / dipeptide transmembrane transporter activity / antibacterial innate immune response / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beale, J.H. / Newstead, S. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.8 KB | Display | ![]() |
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PDB format | ![]() | 201.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.4 KB | Display | ![]() |
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Full document | ![]() | 485.8 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Nonpolymer details | CITRATE (CIT): FROM CRYSTALLIS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() 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.
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Displacement parameters | Biso mean: 75.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.465 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→47.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.84→2.98 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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