[English] 日本語
Yorodumi- PDB-8f23: The crystal structure of a rationally designed zinc sensor based ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f23 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a rationally designed zinc sensor based on maltose binding protein - Apo conformation | ||||||
Components | Zinc Sensor protein | ||||||
Keywords | METAL BINDING PROTEIN / zinc / sensing / Xe NMR | ||||||
Function / homology | Function and homology information carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Zhao, Z. / Zhou, M. / Zemerov, S.d. / Marmorstein, R. / Dmochowski, I.J. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Chem Sci / Year: 2023 Title: Rational design of a genetically encoded NMR zinc sensor. Authors: Zhao, Z. / Zhou, M. / Zemerov, S.D. / Marmorstein, R. / Dmochowski, I.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8f23.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8f23.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 8f23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f23_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8f23_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 8f23_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 8f23_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/8f23 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f23 | HTTPS FTP |
-Related structure data
Related structure data | 8etbC 1ompS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40222.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, Z5632, ECs5017 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEY0 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M sodium formate, pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→68.43 Å / Num. obs: 25254 / % possible obs: 98.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 42.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 5.9 % / Num. unique obs: 1328 / CC1/2: 0.497 / % possible all: 77.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1omp Resolution: 1.93→56.62 Å / SU ML: 0.2993 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1192 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→56.62 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|