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Yorodumi- PDB-2r9g: Crystal structure of the C-terminal fragment of AAA ATPase from E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r9g | ||||||
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Title | Crystal structure of the C-terminal fragment of AAA ATPase from Enterococcus faecium | ||||||
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 | post-AAA+ oligomerization domain-like / DNA polymerase III clamp loader subunits, C-terminal domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / ACETATE ION / : Function and homology information | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Ramagopal, U.A. / Patskovsky, Y. / Bonanno, J.B. / Shi, W. / Toro, R. / Meyer, A.J. / Rutter, M. / Wu, B. / Groshong, C. / Gheyi, T. ...Ramagopal, U.A. / Patskovsky, Y. / Bonanno, J.B. / Shi, W. / Toro, R. / Meyer, A.J. / Rutter, M. / Wu, B. / Groshong, C. / Gheyi, T. / 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 AAA ATPase from Enterococcus faecium. Authors: Ramagopal, U.A. / Patskovsky, Y. / Bonanno, J.B. / Shi, W. / Toro, R. / Meyer, A.J. / Rutter, M. / Wu, B. / Groshong, C. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r9g.cif.gz | 594.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r9g.ent.gz | 496 KB | Display | PDB format |
PDBx/mmJSON format | 2r9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r9g_validation.pdf.gz | 600 KB | Display | wwPDB validaton report |
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Full document | 2r9g_full_validation.pdf.gz | 630.1 KB | Display | |
Data in XML | 2r9g_validation.xml.gz | 111 KB | Display | |
Data in CIF | 2r9g_validation.cif.gz | 156.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/2r9g ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r9g | HTTPS FTP |
-Related structure data
Related structure data | 2qw6S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 238 - 422 / Label seq-ID: 12 - 196
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-Components
#1: Protein | Mass: 22719.553 Da / Num. of mol.: 16 / Fragment: C-terminal domain: Residues 230-422 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: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / #4: 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: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 294 K / pH: 7.5 Details: 100mM HEPES pH 7.5, 25% PEG 3350, 200mM Ammonium acetate, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 202788 / % possible obs: 87.3 % / Observed criterion σ(I): -0.5 / Redundancy: 3.6 % / Biso Wilson estimate: 33.04 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.091 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.54 / % possible all: 44.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QW6 Resolution: 2.09→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.794 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.208 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1271 / Refine-ID: X-RAY DIFFRACTION
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