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Yorodumi- PDB-1z67: Structure of Homeodomain-like Protein of Unknown Function S4005 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z67 | ||||||
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Title | Structure of Homeodomain-like Protein of Unknown Function S4005 from Shigella flexneri | ||||||
Components | hypothetical protein S4005 | ||||||
Keywords | Structural Genomics / Unknown Function / hypothetical protein / Shigella flexneri / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | YidB-like / Protein of unknown function DUF937 / YidB-like / Bacterial protein of unknown function (DUF937) / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Shigella flexneri 2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Osipiuk, J. / Maltseva, N. / Dementieva, I. / Clancy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Structure of YidB protein from Shigella flexneri shows a new fold with homeodomain motif. Authors: Osipiuk, J. / Maltseva, N. / Dementieva, I. / Clancy, S. / Collart, F. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S).AUTHOR STATES THAT BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT YET KNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z67.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z67.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1z67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z67_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 1z67_full_validation.pdf.gz | 424.4 KB | Display | |
Data in XML | 1z67_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 1z67_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/1z67 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/1z67 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14234.623 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Species: Shigella flexneri / Strain: 2457T / Gene: yidB / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q83IZ7, UniProt: A0A384K8I9*PLUS |
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#2: Chemical | ChemComp-NA / |
#3: 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 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris, 2 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 7, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→40 Å / Num. all: 17111 / Num. obs: 17111 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 39.2 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.14 / Num. unique all: 291 / % possible all: 26.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→40 Å / Cor.coef. Fo:Fc: 0.969 / SU B: 2.09 / SU ML: 0.037 / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
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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: 22.941 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.451→1.488 Å / Total num. of bins used: 20
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