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Yorodumi- PDB-2xut: Crystal structure of a proton dependent oligopeptide (POT) family... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xut | ||||||
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Title | Crystal structure of a proton dependent oligopeptide (POT) family transporter. | ||||||
Components | PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / MEMBRANE PROTEIN / MAJOR FACILITATOR SUPERFAMILY TRANSPORTER / PROTON COUPLED PEPTIDE TRANSPORT | ||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | SHEWANELLA ONEIDENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.62 Å | ||||||
Authors | Newstead, S. / Drew, D. / Cameron, A.D. / Postis, V.L. / Xia, X. / Fowler, P.W. / Ingram, J.C. / Carpenter, E.P. / Sansom, M.S.P. / McPherson, M.J. ...Newstead, S. / Drew, D. / Cameron, A.D. / Postis, V.L. / Xia, X. / Fowler, P.W. / Ingram, J.C. / Carpenter, E.P. / Sansom, M.S.P. / McPherson, M.J. / Baldwin, S.A. / Iwata, S. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Crystal Structure of a Prokaryotic Homologue of the Mammalian Oligopeptide-Proton Symporters, Pept1 and Pept2. Authors: Newstead, S. / Drew, D. / Cameron, A.D. / Postis, V.L. / Xia, X. / Fowler, P.W. / Ingram, J.C. / Carpenter, E.P. / Sansom, M.S.P. / McPherson, M.J. / Baldwin, S.A. / Iwata, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xut.cif.gz | 462.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xut.ent.gz | 400.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/2xut ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xut | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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: 57684.824 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Strain: MR-1 / Plasmid: PWALDO-GFPE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q8EKT7 Compound details | ENGINEERED RESIDUE IN CHAIN A, THR 2 TO ASN ENGINEERED RESIDUE IN CHAIN A, THR 3 TO SER ENGINEERED ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.49 Å3/Da / Density % sol: 80 % Description: REFINEMENT WAS CARRIED OUT USING ANISOTROPIC TRUNCATION OF THE OBSERVED STRUCTURE FACTORS TO 4.3 A ALONG THE A AND B AXES, AND 3.6 ALONG C |
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Crystal grow | pH: 6.5 / Details: 30% PEG 300, 0.1M MES PH 6.50 AND 0.1M NACL |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 18, 2009 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.62→35.5 Å / Num. obs: 47021 / % possible obs: 93.8 % / Observed criterion σ(I): 1.1 / Redundancy: 2 % / Biso Wilson estimate: 105.41 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.1 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 3.62→35.47 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE MODEL WAS BUILT AND REFINED USING DATA WITH ANISOTROPIC TRUNCATION OF THE OBSERVED STRUCTURE A AND B AXES, WHILST KEEPING THE C AXIS AT 3.6A.
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Displacement parameters | Biso mean: 252.95 Å2
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Refine analyze | Luzzati coordinate error obs: 1.877 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.62→35.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.62→3.76 Å / Total num. of bins used: 14
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Refinement TLS params. | L33: 16.6309 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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