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Yorodumi- PDB-2pcj: Crystal structure of ABC transporter (aq_297) From Aquifex Aeolic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pcj | ||||||
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Title | Crystal structure of ABC transporter (aq_297) From Aquifex Aeolicus VF5 | ||||||
Components | Lipoprotein-releasing system ATP-binding protein lolD | ||||||
Keywords | HYDROLASE / ABC TRANSPORTER / ATP-BINDING PROTEIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ABC transporter (aq_297) From Aquifex Aeolicus VF5 Authors: Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pcj.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pcj.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/2pcj ftp://data.pdbj.org/pub/pdb/validation_reports/pc/2pcj | HTTPS FTP |
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-Related structure data
Related structure data | 1f3oS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24923.045 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CONDON PLUS (DE3)-RIL References: UniProt: O66646, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances #2: Chemical | ChemComp-SO3 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 20% isopropanol, 0.1 M Na Citrate, 16% PEG 4000, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.9794 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 17, 2006 / Details: RH Coated Bent-Cyrindrical MIRROR |
Radiation | Monochromator: SI 1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 46193 / Num. obs: 46193 / % possible obs: 99.3 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.044 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.19 / Num. unique all: 4282 / Rsym value: 0.188 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F3O Resolution: 1.7→45.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3052149.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.9807 Å2 / ksol: 0.369103 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 17.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→45.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
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Xplor file |
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