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Yorodumi- PDB-3k9h: Crystal structure of a plasmid partition protein from borrelia bu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k9h | ||||||
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Title | Crystal structure of a plasmid partition protein from borrelia burgdorferi at 2.25A resolution | ||||||
Components | PF-32 protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / SSGCID / SBRI / DECODE BIOSTRUCTURES / UW / NIH / NIAID / BORELLIA BURGDORFERI / PLASMID PARTITION PROTEIN / Plasmid / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | : / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PF-32 protein Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a plasmid partition protein from borrelia burgdorferi at 2.25A resolution Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Edwards, T. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k9h.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k9h.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 3k9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k9h_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 3k9h_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 3k9h_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 3k9h_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/3k9h ftp://data.pdbj.org/pub/pdb/validation_reports/k9/3k9h | HTTPS FTP |
-Related structure data
Related structure data | 3k9gS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 6 / Auth seq-ID: 5 - 250 / Label seq-ID: 26
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-Components
#1: Protein | Mass: 30984.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Strain: B31 / Gene: PF-32, BB_S35 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68233 #2: Chemical | #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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: INDEX SCREEN G5: 25% PEG 3350, TRIS PH 8.5, 200MM LI2SO4, BOBUA.01478.A AT 33MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30.2 Å / Num. all: 29899 / Num. obs: 28812 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 35.22 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.08 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2187 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3K9G, iodide soak Resolution: 2.25→30.2 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.645 / SU ML: 0.144 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.213 / 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: 18.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→30.2 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2960 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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