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Yorodumi- PDB-1gaj: CRYSTAL STRUCTURE OF A NUCLEOTIDE-FREE ATP-BINDING CASSETTE FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gaj | ||||||
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Title | CRYSTAL STRUCTURE OF A NUCLEOTIDE-FREE ATP-BINDING CASSETTE FROM AN ABC TRANSPORTER | ||||||
Components | HIGH-AFFINITY BRANCHED CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / active transport / ATPase / nucleotide-binding domain | ||||||
Function / homology | Function and homology information amino acid transport / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Karpowich, N. / Yuan, Y.-R. / Dai, P.L. / Martsinkevich, O. / Millen, L. / Thomas, P.J. / Hunt, J.F. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter. Authors: Karpowich, N. / Martsinkevich, O. / Millen, L. / Yuan, Y.R. / Dai, P.L. / MacVey, K. / Thomas, P.J. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gaj.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gaj.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gaj_validation.pdf.gz | 462.3 KB | Display | wwPDB validaton report |
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Full document | 1gaj_full_validation.pdf.gz | 472.4 KB | Display | |
Data in XML | 1gaj_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1gaj_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/1gaj ftp://data.pdbj.org/pub/pdb/validation_reports/ga/1gaj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29028.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL+ / References: GenBank: 1591902, UniProt: Q58663*PLUS |
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-Non-polymers , 5 types, 141 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.04 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES-Cl, (NH4)2SO4, PEG 400, T-butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.06884 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06884 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 15956 / Num. obs: 13129 / % possible obs: 82.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 39.9 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 44.16 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 19 % / Rmerge(I) obs: 0.43 / % possible all: 69 |
Reflection | *PLUS Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: X-PLOR 3.851
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Refinement step | Cycle: LAST / Resolution: 2.5→100 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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