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Yorodumi- PDB-3hwu: Crystal structure of Putative DNA-binding protein (YP_299413.1) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hwu | ||||||
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Title | Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutrophA JMP134 at 1.30 A resolution | ||||||
Components | Putative DNA-binding protein | ||||||
Keywords | Structural Genomics / Unknown function / YP_299413.1 / Putative DNA-binding protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Domain of unknown function (DUF296) | ||||||
Function / homology | Predicted DNA-binding protein with PD1-like DNA-binding motif / PPC domain / Plants and Prokaryotes Conserved (PCC) domain / PPC domain profile profile. / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / PPC domain-containing protein Function and homology information | ||||||
Biological species | Ralstonia eutropha (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutropha JMP134 at 1.30 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hwu.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hwu.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hwu_validation.pdf.gz | 419.6 KB | Display | wwPDB validaton report |
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Full document | 3hwu_full_validation.pdf.gz | 421.2 KB | Display | |
Data in XML | 3hwu_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3hwu_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/3hwu ftp://data.pdbj.org/pub/pdb/validation_reports/hw/3hwu | HTTPS FTP |
-Related structure data
Similar structure data | |
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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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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 16387.719 Da / Num. of mol.: 1 / Fragment: sequence database residues 28-173 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_B5223, YP_299413.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46QL5 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2000M NaCl, 20.0000% PEG-1000, 0.1M Na,K-Phosphate pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97929,0.97918 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2009 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.3→26.948 Å / Num. obs: 29085 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 2.71 % / Biso Wilson estimate: 11.177 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 13.78 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.3→26.948 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.308 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.042 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.UNKNOWN ELECTRON DENSITY IS OBSERVED NEAR RESIDUE 117, 119 AND 133 DURING REFINEMENT.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.94 Å2 / Biso mean: 15.307 Å2 / Biso min: 3.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→26.948 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.302→1.336 Å / Total num. of bins used: 20
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