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- PDB-4h5f: Crystal structure of an amino acid ABC transporter substrate-bind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h5f | ||||||
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Title | Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 1 | ||||||
![]() | Amino acid ABC superfamily ATP binding cassette transporter, binding protein | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine, form 1 Authors: Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 401.8 KB | Display | ![]() |
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PDB format | ![]() | 333.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1wdnS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26175.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 9 types, 545 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-CL / | ![]() #4: Chemical | ChemComp-PEG / ![]() #5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ChemComp-PGE / ![]() #7: Chemical | ChemComp-ARG / ![]() #8: Chemical | ChemComp-ACT / ![]() #9: Chemical | ChemComp-EDO / | ![]() #10: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | THE ELECTRON DENSITY CLEARLY SUPPORTS HISTIDINE AT POSITION 136 RATHER THAN ARGININE. HOWEVER, NO ...THE ELECTRON DENSITY CLEARLY SUPPORTS HISTIDINE AT POSITION 136 RATHER THAN ARGININE. HOWEVER, NO SUITABLE SEQUENCE IN THE GENOME DATABASES WAS FOUND. HIS 136 IS ASSUMED TO BE A SEQUENCE MUTATION IN THE GENE WE WORKED WITH, RELATIVE TO THE DATABASE SEQUENCE D6ZRZ2. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, PEG 2K MME 30% (w/v), 2% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 30, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→91.461 Å / Num. all: 254378 / Num. obs: 85607 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / Num. unique all: 36813 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1WDN Resolution: 1.9→91.461 Å / Cross valid method: random / σ(F): 1.35 / Phase error: 25.91 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→91.461 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: 49.9538 Å / Origin y: 43.102 Å / Origin z: 61.8556 Å
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Refinement TLS group | Selection details: all |