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Yorodumi- PDB-3zrx: The high resolution structure of a dimeric Hamp-Dhp fusion displa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zrx | ||||||
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Title | The high resolution structure of a dimeric Hamp-Dhp fusion displays strong asymmetry | ||||||
Components | AF1503 PROTEIN, OSMOLARITY SENSOR PROTEIN ENVZ | ||||||
Keywords | SIGNALING PROTEIN / OSMOREGULATION / OMPR / OMPC | ||||||
Function / homology | Function and homology information response to osmotic stress / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity ...response to osmotic stress / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å | ||||||
Authors | Zeth, K. / Hulko, M. / Martin, J. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Mechanism of Regulation of Receptor Histidine Kinases. Authors: Ferris, H.U. / Dunin-Horkawicz, S. / Hornig, N. / Hulko, M. / Martin, J. / Schultz, J.E. / Zeth, K. / Lupas, A.N. / Coles, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zrx.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zrx.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/3zrx ftp://data.pdbj.org/pub/pdb/validation_reports/zr/3zrx | HTTPS FTP |
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-Related structure data
Related structure data | 2lfrC 2lfsC 3zrvC 3zrwC 2asmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13083.843 Da / Num. of mol.: 2 / Fragment: RESIDUES 278-327,229-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI (E. coli) Strain: DSM 4304, K-12 / Description: PCR FROM E. COLI WT DNA AND A. FULGIDUS WT DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O28769, UniProt: P0AEJ4, histidine kinase #2: Water | ChemComp-HOH / | Sequence details | THIS PROTEIN STRUCTURE COMPRISES RESIDUES OF THE PROTEIN AF1503 FROM A. FULGIDUS AND THE OSMOLARITY ...THIS PROTEIN STRUCTURE COMPRISES RESIDUES OF THE PROTEIN AF1503 FROM A. FULGIDUS AND THE OSMOLARITY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.98 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 0.02 M CALCIUM CHLORIDE 0.1 M SODIUM ACETATE 30% MPD, PH4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.068 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.068 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→20 Å / Num. obs: 52510 / % possible obs: 90.7 % / Observed criterion σ(I): 1.25 / Redundancy: 4.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 2ASM Resolution: 1.25→18.84 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.784 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.051 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.428 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→18.84 Å
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Refine LS restraints |
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