+Open data
-Basic information
Entry | Database: PDB / ID: 6k5p | ||||||
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Title | Structure of mosquito-larvicidal Binary toxin receptor, Cqm1 | ||||||
Components | Binary toxin receptor protein | ||||||
Keywords | PROTEIN BINDING / Amylomaltase / GH13_17 subfamily / Receptor for BinAB toxin / Cqm1 | ||||||
Function / homology | Function and homology information catalytic activity / membrane => GO:0016020 / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Culex quinquefasciatus (southern house mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å | ||||||
Authors | Kumar, V. / Sharma, M. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2019 Title: Crystal structure of BinAB toxin receptor (Cqm1) protein and molecular dynamics simulations reveal the role of unique Ca(II) ion. Authors: Sharma, M. / Kumar, V. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Mosquito-larvicidal binary toxin receptor protein (Cqm1): crystallization and X-ray crystallographic analysis. Authors: Sharma, M. / Lakshmi, A. / Gupta, G.D. / Kumar, V. #2: Journal: Insect Biochem. Mol. Biol. / Year: 2018 Title: Receptor protein of Lysinibacillus sphaericus mosquito-larvicidal toxin displays amylomaltase activity. Authors: Sharma, M. / Gupta, G.D. / Kumar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k5p.cif.gz | 939.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k5p.ent.gz | 776.7 KB | Display | PDB format |
PDBx/mmJSON format | 6k5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/6k5p ftp://data.pdbj.org/pub/pdb/validation_reports/k5/6k5p | HTTPS FTP |
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-Related structure data
Related structure data | 3wy1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | Authors state that the protein 6K5P does not exist as tetramer, |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 64744.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Culex quinquefasciatus (southern house mosquito) Gene: Cqm1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Star (D3) / References: UniProt: B0X223*PLUS |
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-Non-polymers , 6 types, 2333 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
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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: 2.24 Å3/Da / Density % sol: 48.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5mM CoCl2, 5mM CdCl2, 5mM MgCl2, 5mM NiCl2, 0.1mM HEPES pH 7.5, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 3, 2018 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.805→39.23 Å / Num. obs: 201511 / % possible obs: 93.9 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.09 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.805→1.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 31009 / CC1/2: 0.929 / Rpim(I) all: 0.318 / Rrim(I) all: 0.621 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WY1 Resolution: 1.805→29.828 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.38 Details: Metal-ligand distance were not restrained. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. Data at 1.9A was used for obtaining initial phases by MRSAD method. High ...Details: Metal-ligand distance were not restrained. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. Data at 1.9A was used for obtaining initial phases by MRSAD method. High resolution data acquired at 0.9795A was used for structure refinement.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.805→29.828 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.805→1.823 Å
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Refinement TLS params. | Method: refined / Origin x: -17.6037 Å / Origin y: -1.0327 Å / Origin z: 74.8901 Å
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Refinement TLS group | Selection details: all |