+Open data
-Basic information
Entry | Database: PDB / ID: 4q7e | ||||||
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Title | Non-phosphorylated HemR Receiver Domain from Leptospira biflexa | ||||||
Components | Response regulator of a two component regulatory system | ||||||
Keywords | SIGNALING PROTEIN / Response Regulator / DNA BINDING PROTEIN | ||||||
Function / homology | Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Leptospira biflexa serovar Patoc (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.441 Å | ||||||
Authors | Morero, N.R. / Buschiazzo, A. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2014 Title: HemR is an OmpR/PhoB-like response regulator from Leptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes. Authors: Morero, N.R. / Botti, H. / Nitta, K.R. / Carrion, F. / Obal, G. / Picardeau, M. / Buschiazzo, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q7e.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q7e.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 4q7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/4q7e ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7e | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14851.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira biflexa serovar Patoc (bacteria) Strain: Patoc / Gene: LBF_1368 / Production host: Escherichia coli (E. coli) / References: UniProt: B0SGG3 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 2.04 Å3/Da / Density % sol: 39.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2M ammonium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Varimax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.441→66.977 Å / Num. all: 40835 / Num. obs: 40835 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.68 Å2 / Rsym value: 0.033 / Net I/σ(I): 22.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.441→35.847 Å / FOM work R set: 0.9055 / SU ML: 0.13 / σ(F): 1.21 / Phase error: 16.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 158.08 Å2 / Biso mean: 21.17 Å2 / Biso min: 6.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.441→35.847 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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