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Yorodumi- PDB-5cof: Crystal structure of Uncharacterised protein Q1R1X2 from Escheric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cof | ||||||
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Title | Crystal structure of Uncharacterised protein Q1R1X2 from Escherichia coli UTI89 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Bacteriocin / sporulation / DUF1706 / cell cycle | ||||||
Function / homology | Protein of unknown function DUF1706 / Protein of unknown function (DUF1706) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / metal ion binding / Uncharacterized protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Taylor, J.D. / Hare, S. / Matthews, S.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide. Authors: Taylor, J.D. / Taylor, G. / Hare, S.A. / Matthews, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cof.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cof.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 5cof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cof_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 5cof_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 5cof_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5cof_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/5cof ftp://data.pdbj.org/pub/pdb/validation_reports/co/5cof | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19931.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain UTI89 / UPEC) (bacteria) Strain: UTI89 / UPEC / Gene: UTI89_P066 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1R1X2 |
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-Non-polymers , 5 types, 359 molecules
#2: Chemical | ChemComp-MPD / ( | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 60 mM Magnesium chloride hexahydrate, 60 mM Calcium chloride dihydrate, 0.1 M imidazole, 0.1 M MES monohydrate, pH 6.5, 12.5% MPD, 12.5 % PEG 1000, 12.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→41.34 Å / Num. obs: 38126 / % possible obs: 98.93 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.35→1.385 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.5 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→41.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.246 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.042 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.489 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→41.29 Å
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