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Yorodumi- PDB-3k9g: CRYSTAL STRUCTURE OF A PLASMID PARTITION PROTEIN FROM BORRELIA BU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k9g | ||||||
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Title | CRYSTAL STRUCTURE OF A PLASMID PARTITION PROTEIN FROM BORRELIA BURGDORFERI AT 2.25A RESOLUTION, iodide soak | ||||||
Components | PF-32 protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / SSGCID / SBRI / DECODE BIOSTRUCTURES / UW / NIH / NIAID / BORELLIA BURGDORFERI / PLASMID PARTITION PROTEIN / IODIDE / SAD PHASING / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / IODIDE ION / PF-32 protein Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.25 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: J Struct Funct Genomics / Year: 2011 Title: SAD phasing using iodide ions in a high-throughput structural genomics environment. Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k9g.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k9g.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k9g_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 3k9g_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 3k9g_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3k9g_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/3k9g ftp://data.pdbj.org/pub/pdb/validation_reports/k9/3k9g | HTTPS FTP |
-Related structure data
Related structure data | 3km3C 3kw3C 3luzC 3menC 3njbC 3o2eC 3oibC 3p96C 3pfdC 3pm6C C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30984.820 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-IOD / #4: 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: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: INDEX SCREEN A10: 3M NACL, 100MM BISTRIS PH 6.5 EXCHANGED IN 2M NACL, 1M KI, 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: Oct 5, 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: 16030 / Num. obs: 15985 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25 % / Biso Wilson estimate: 41.45 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 34.53 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 13 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 5 / Num. unique all: 1158 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→30.2 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.088 / SU ML: 0.133 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / 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: 23.82 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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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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