[English] 日本語
Yorodumi- PDB-2a0b: HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a0b | ||||||
---|---|---|---|---|---|---|---|
Title | HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ARCB FROM ESCHERICHIA COLI | ||||||
Components | HPT DOMAIN | ||||||
Keywords | SENSORY TRANSDUCTION / HISTIDINE KINASE / PHOSPHOTRANSFER / TWO-COMPONENT SYSTEM / FOUR-HELIX BUNDLE | ||||||
Function / homology | Function and homology information peptidyl-histidine phosphorylation / response to oxygen levels / histidine kinase / plasma membrane => GO:0005886 / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / protein autophosphorylation / regulation of DNA-templated transcription / signal transduction / ATP binding ...peptidyl-histidine phosphorylation / response to oxygen levels / histidine kinase / plasma membrane => GO:0005886 / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / protein autophosphorylation / regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.57 Å | ||||||
Authors | Kato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Refined structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor kinase ArcB from Escherichia coli at 1.57 A resolution. Authors: Kato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T. #1: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Insights Into Multistep Phosphorelay from the Crystal Structure of the C-Terminal Hpt Domain of Arcb Authors: Kato, M. / Mizuno, T. / Shimizu, T. / Hakoshima, T. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary X-Ray Analysis of a Histidine Kinase Domain of the Anaerobic Sensor Protein Arcb from Escherichia Coli Authors: Kato, M. / Ishige, K. / Mizuno, T. / Shimizu, T. / Hakoshima, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a0b.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a0b.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 2a0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a0b_validation.pdf.gz | 405 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2a0b_full_validation.pdf.gz | 408.8 KB | Display | |
Data in XML | 2a0b_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2a0b_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/2a0b ftp://data.pdbj.org/pub/pdb/validation_reports/a0/2a0b | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14013.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PSU2DH / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): DZ225 References: UniProt: P22763, UniProt: P0AEC3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: THE FURTHER REFINEMENT OF 1A0B | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.1 Details: PROTEIN WAS CRYSTALLIZED FROM 12.5% PEGMME 550, 5 MM ZNSO4, 50 MM ACETIC ACID/SODIUM ACETATE BUFFER, PH 4.1 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.57 Å / Num. obs: 16338 / % possible obs: 94.7 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 66 |
Reflection shell | Resolution: 1.57→1.7 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / % possible all: 89 |
Reflection | *PLUS % possible obs: 95 % / Num. measured all: 98202 |
Reflection shell | *PLUS % possible obs: 89 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.57→6 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 16036 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.57 Å / Lowest resolution: 1.63 Å / Rfactor Rfree: 0.299 / Rfactor Rwork: 0.277 |