+Open data
-Basic information
Entry | Database: PDB / ID: 5xly | ||||||
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Title | Crystal structure of CheR1 in complex with c-di-GMP-bound MapZ | ||||||
Components |
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Keywords | TRANSFERASE / signaling / methyltransferase | ||||||
Function / homology | Function and homology information protein-glutamate O-methyltransferase / protein-glutamate O-methyltransferase activity / cyclic-di-GMP binding / methylation Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.763 Å | ||||||
Authors | Yuan, Z. / Zhu, Y. / Gu, L. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Structural basis for the regulation of chemotaxis by MapZ in the presence of c-di-GMP Authors: Zhu, Y. / Yuan, Z. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xly.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xly.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 5xly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xly_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5xly_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5xly_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 5xly_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/5xly ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xly | HTTPS FTP |
-Related structure data
-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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-Components
#1: Protein | Mass: 31617.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: cheR1, PA3348 / Production host: Escherichia coli (E. coli) References: UniProt: O87131, protein-glutamate O-methyltransferase | ||
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#2: Protein | Mass: 15664.526 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4608 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVI1 | ||
#3: Chemical | #4: 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: 2.48 Å3/Da / Density % sol: 50.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 15% 2-propanol 0.1M Sodium citrate 5.0 10% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→68.36 Å / Num. obs: 44834 / % possible obs: 97.6 % / Redundancy: 1.9 % / Net I/σ(I): 4.39 |
-Processing
Software |
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Refinement | Resolution: 1.763→19.45 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.98 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.763→19.45 Å
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Refine LS restraints |
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LS refinement shell |
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