[English] 日本語
Yorodumi- PDB-1y7y: High-resolution crystal structure of the restriction-modification... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y7y | ||||||
---|---|---|---|---|---|---|---|
Title | High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila | ||||||
Components | C.AhdI | ||||||
Keywords | Transcription regulator / HELIX-TURN-HELIX / DNA-BINDING PROTEIN / TRANSCRIPTIONAL REGULATOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aeromonas hydrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | McGeehan, J.E. / Streeter, S.D. / Papapanagiotou, I. / Fox, G.C. / Kneale, G.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila. Authors: McGeehan, J.E. / Streeter, S.D. / Papapanagiotou, I. / Fox, G.C. / Kneale, G.G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and preliminary X-ray analysis of the controller protein C.AhdI from Aeromonas hydrophilia Authors: McGeehan, J.E. / Streeter, S. / Cooper, J.B. / Mohammed, F. / Fox, G.C. / Kneale, G.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1y7y.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1y7y.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 1y7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y7y_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1y7y_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 1y7y_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1y7y_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y7y ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y7y | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS WHICH MAKE UP THE BIOLOGICAL DIMER |
-Components
#1: Protein | Mass: 8382.575 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q7X0F0 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, IMIDAZOLE-MALATE, 2-METHYL-2,4-PENTANEDIOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.904989 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 21, 2003 / Details: MIRRORS |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.904989 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→45.57 Å / Num. all: 14937 / Num. obs: 14302 / % possible obs: 95.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1561 / Rsym value: 0.181 / % possible all: 95.7 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Mutant I58M of C.AhdI, SeMet MAD to 2.5A Resolution: 1.69→18.4 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→18.4 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|