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- PDB-6k5p: Structure of mosquito-larvicidal Binary toxin receptor, Cqm1 -

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Basic information

Entry
Database: PDB / ID: 6k5p
TitleStructure of mosquito-larvicidal Binary toxin receptor, Cqm1
ComponentsBinary toxin receptor protein
KeywordsPROTEIN BINDING / Amylomaltase / GH13_17 subfamily / Receptor for BinAB toxin / Cqm1
Function / homology
Function and homology information


alpha-glucosidase / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / : / : / alpha-glucosidase
Similarity search - Component
Biological speciesCulex quinquefasciatus (southern house mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsKumar, 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
DepositionMay 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Binary toxin receptor protein
B: Binary toxin receptor protein
C: Binary toxin receptor protein
D: Binary toxin receptor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,22433
Polymers258,9804
Non-polymers2,24429
Water41,5072304
1
A: Binary toxin receptor protein
B: Binary toxin receptor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,74817
Polymers129,4902
Non-polymers1,25915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Binary toxin receptor protein
D: Binary toxin receptor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,47616
Polymers129,4902
Non-polymers98614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-197 kcal/mol
Surface area74330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.181, 191.486, 205.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the protein 6K5P does not exist as tetramer,

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Binary toxin receptor 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 / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mg
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: Cd
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2304 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE 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 KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS VTO94530.1.1 FOR THE PROTEIN. DNA/PROTEIN SEQUENCE HAS BEEN DEPOSITED THROUGH ENA PROJECT (LR58805.1)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 3, 2018
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERPHASER-EPphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WY1

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 9858 4.91 %Random Selelction
Rwork0.183 ---
obs0.1851 200966 93.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.805→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17178 0 44 2304 19526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond0.00617703
X-RAY DIFFRACTIONf_angle0.82124066
X-RAY DIFFRACTIONf_dihedral_angle_d15.0726389
X-RAY DIFFRACTIONf_chiral_restr0.0532469
X-RAY DIFFRACTIONf_plane_restr0.0063163
LS refinement shellResolution: 1.805→1.823 Å
RfactorNum. reflection% reflection
Rfree0.95 403 -
Rwork0.1797 --
obs0.1459 6917 1 %
Refinement TLS params.Method: refined / Origin x: -17.6037 Å / Origin y: -1.0327 Å / Origin z: 74.8901 Å
111213212223313233
T0.1267 Å20.0071 Å2-0.0162 Å2-0.1878 Å20.0049 Å2--0.1841 Å2
L0.0588 °20.0008 °2-0.0427 °2-0.2145 °20.1537 °2--0.2722 °2
S-0.0097 Å °-0.0021 Å °-0.0057 Å °0.0399 Å °0.0188 Å °-0.0276 Å °0.0567 Å °-0.0194 Å °-0.0088 Å °
Refinement TLS groupSelection details: all

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