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- PDB-4d1d: STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORT... -
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Open data
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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. | ||||||
![]() | HYDANTOIN TRANSPORT PROTEIN | ||||||
![]() | TRANSPORT PROTEIN / MEMBRANE PROTEIN TRANSPORTER / SUBSTRATE-BOUND / OCCLUDED STATE | ||||||
Function / homology | ![]() nucleobase transmembrane transporter activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weyand, S. / Brueckner, F. / Geng, T. / Drew, D. / Iwata, S. / Henderson, P.J.F. / Cameron, A.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.8 KB | Display | ![]() |
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PDB format | ![]() | 161.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 467.6 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d1aSC ![]() 4d1bC ![]() 4d1cC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |