+Open data
-Basic information
Entry | Database: PDB / ID: 3sk7 | ||||||
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Title | Crystal Structure of V. cholerae SeqA | ||||||
Components | Protein SeqA | ||||||
Keywords | REPLICATION INHIBITOR / Sequestration / Negative regulator / DNA replication initiation / DNA binding | ||||||
Function / homology | Replication modulator SeqA, C-terminal DNA-binding domain / Replication modulator SeqA, C-terminal DNA-binding domain / Up-down Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Chung, Y.S. / Guarne, A. | ||||||
Citation | Journal: To be Published Title: Investigating the aggregational property of SeqAvibrio in the absence of the oligomerization domain Authors: Chung, Y.S. / Guarne, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sk7.cif.gz | 173.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sk7.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 3sk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sk7_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 3sk7_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 3sk7_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3sk7_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/3sk7 ftp://data.pdbj.org/pub/pdb/validation_reports/sk/3sk7 | HTTPS FTP |
-Related structure data
Related structure data | 3fmtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT NO QUATERNARY STRUCTURES WERE DETECTED. |
-Components
#1: Protein | Mass: 13285.413 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: A5C_2175, seqA / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A3GNC8 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.46→50 Å / Num. obs: 35671 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.266 | ||||||||||||||||||
Reflection shell | Resolution: 1.46→1.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4.403 / Rsym value: 0.462 / % possible all: 98.3 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 3FMT Resolution: 1.5→34.918 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.81 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.972 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→34.918 Å
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Refine LS restraints |
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LS refinement shell |
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