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Yorodumi- PDB-6blb: 1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-... -
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-Basic information
Entry | Database: PDB / ID: 6blb | ||||||
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Title | 1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-dependent DNA Helicase (RuvB) from Pseudomonas aeruginosa in Complex with ADP | ||||||
Components | Holliday junction ATP-dependent DNA helicase RuvB | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Holliday Junction ATP-dependent DNA Helicase / ADP | ||||||
Function / homology | Function and homology information cellular response to chromate / cellular response to selenite ion / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA helicase / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-dependent DNA Helicase (RuvB) from Pseudomonas aeruginosa in Complex with ADP. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6blb.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6blb.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 6blb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/6blb ftp://data.pdbj.org/pub/pdb/validation_reports/bl/6blb | HTTPS FTP |
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-Related structure data
Related structure data | 1in4S 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: 39253.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ruvB, PA0967 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q51426, DNA helicase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-PGE / |
#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: 2.04 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 8.6 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3, screen: Classics II (D3), 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2017 / Details: C(111) |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→30 Å / Num. obs: 26154 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.028 / Rrim(I) all: 0.081 / Rsym value: 0.076 / Χ2: 1.01 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1311 / CC1/2: 0.811 / Rpim(I) all: 0.291 / Rrim(I) all: 0.849 / Rsym value: 0.797 / Χ2: 1.009 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IN4 Resolution: 1.88→28.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.796 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.136 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.916 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→28.64 Å
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Refine LS restraints |
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