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Yorodumi- PDB-4d1d: STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d1d | ||||||
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Title | STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORTER with the inhibitor 5-(2-naphthylmethyl)-L-hydantoin. | ||||||
Components | HYDANTOIN TRANSPORT PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / MEMBRANE PROTEIN TRANSPORTER / SUBSTRATE-BOUND / OCCLUDED STATE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MICROBACTERIUM LIQUEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Weyand, S. / Brueckner, F. / Geng, T. / Drew, D. / Iwata, S. / Henderson, P.J.F. / Cameron, A.D. | ||||||
Citation | Journal: Embo J. / Year: 2014 Title: Molecular Mechanism of Ligand Recognition by Membrane Transport Protein, Mhp1. Authors: Simmons, K.J. / Jackson, S.M. / Brueckner, F. / Patching, S.G. / Beckstein, O. / Ivanova, E. / Geng, T. / Weyand, S. / Drew, D. / Lanigan, J. / Sharples, D.J. / Sansom, M.S. / Iwata, S. / ...Authors: Simmons, K.J. / Jackson, S.M. / Brueckner, F. / Patching, S.G. / Beckstein, O. / Ivanova, E. / Geng, T. / Weyand, S. / Drew, D. / Lanigan, J. / Sharples, D.J. / Sansom, M.S. / Iwata, S. / Fishwick, C.W. / Johnson, A.P. / Cameron, A.D. / Henderson, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d1d.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d1d.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 4d1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d1d ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d1d | HTTPS FTP |
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-Related structure data
Related structure data | 4d1aSC 4d1bC 4d1cC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54017.148 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-487 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MICROBACTERIUM LIQUEFACIENS (bacteria) / Strain: AJ3912 / Plasmid: PWALDOGFPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LEMO21 / References: UniProt: D6R8X8 |
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#2: Chemical | ChemComp-5NL / |
#3: Chemical | ChemComp-5ND / |
#4: Chemical | ChemComp-NA / |
Nonpolymer details | 5-(2-NAPHTHYLME |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 74 % / Description: NONE |
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 27-33 % PEG 300, 0.1 M NACL AND 0.1M NA-PHOSPHATE (PH 7.0). NMH WAS ADDED TO THE DROP AS A SATURATED SOLUTION. |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 19, 2011 |
Radiation | Monochromator: SI(III) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→38 Å / Num. obs: 10714 / % possible obs: 97 % / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Biso Wilson estimate: 129.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.7→3.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D1A Resolution: 3.7→37.777 Å / SU ML: 0.65 / σ(F): 0 / Phase error: 37.68 / Stereochemistry target values: ML Details: COORDINATES WERE RESTRAINED TO 2JLN DURING REFINEMENT. COMPOUND WAS A MIXTURE OF D AND L FORMS OF NMH. BOTH BIND EQUALLY WELL. REFINED BOTH AT HALF OCCUPANCY.
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 195 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→37.777 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.0626 Å / Origin y: 16.1843 Å / Origin z: -21.6688 Å
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Refinement TLS group | Selection details: ALL |