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Yorodumi- PDB-2qw6: Crystal structure of the C-terminal domain of an AAA ATPase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qw6 | ||||||
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Title | Crystal structure of the C-terminal domain of an AAA ATPase from Enterococcus faecium DO | ||||||
Components | AAA ATPase, central region | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / ATPASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ATP-binding / Nucleotide-binding | ||||||
Function / homology | Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Up-down Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Bonanno, J.B. / Rutter, M. / Bain, K.T. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the C-terminal domain of an AAA ATPase from Enterococcus faecium DO. Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT THE TETRAMERIC ASSEMBLY SHOWN IN REMARK 350 IS PROBABLE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qw6.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qw6.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 2qw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qw6_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 2qw6_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 2qw6_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2qw6_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/2qw6 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/2qw6 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | probable tetramer |
-Components
#1: Protein | Mass: 11998.666 Da / Num. of mol.: 4 / Fragment: C-terminal domain: Residues 230-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Strain: DO / Gene: EfaeDRAFT_0938 / Plasmid: Modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3XY27 #2: 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: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 Details: 100mM Imidazole pH 6.5, 1M Sodium acetate hydrate, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 29, 2007 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→87.706 Å / Num. all: 22041 / Num. obs: 22041 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3160 / Rsym value: 0.662 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.066 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.261 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.761 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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