+Open data
-Basic information
Entry | Database: PDB / ID: 4ymv | ||||||
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Title | Crystal structure of an amino acid ABC transporter with ATPs | ||||||
Components |
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Keywords | PROTEIN BINDING/TRANSPORT PROTEIN / ABC transporter / two binding sites / substrate specificity / membrane protein complex / PROTEIN BINDING-TRANSPORT PROTEIN complex | ||||||
Function / homology | Function and homology information ABC-type amino acid transporter activity / nitrogen compound transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis MB4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å | ||||||
Authors | Ge, J. / Yu, J. / Yang, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structural basis for substrate specificity of an amino acid ABC transporter Authors: Yu, J. / Ge, J. / Heuveling, J. / Schneider, E. / Yang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ymv.cif.gz | 361.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ymv.ent.gz | 296.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ymv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/4ymv ftp://data.pdbj.org/pub/pdb/validation_reports/ym/4ymv | HTTPS FTP |
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-Related structure data
Related structure data | 4ymsC 4ymtC 4ymuC 4ymwC 4ymxC 3dhwS C: citing same article (ref.) S: Starting model for refinement |
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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: 26821.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis MB4 (bacteria) Strain: MB4 / Gene: GlnQ, TTE0514 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RCC2 #2: Protein | Mass: 24245.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis MB4 (bacteria) Strain: MB4 / Gene: ArtM, TTE0513 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RCC3 #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12% PEG4000, 0.1M NaCl, 0.1M MgCl, 0.1M Na Citrate / PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3→45 Å / Num. obs: 33536 / % possible obs: 98.7 % / Redundancy: 5.5 % / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.2 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DHW Resolution: 3.003→43.508 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.44 / Stereochemistry target values: ML
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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: 3.003→43.508 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: -22.6661 Å / Origin y: 22.7096 Å / Origin z: 32.629 Å
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Refinement TLS group | Selection details: all |