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- PDB-2xz5: MMTS-modified Y53C mutant of Aplysia AChBP in complex with acetyl... -

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Basic information

Entry
Database: PDB / ID: 2xz5
TitleMMTS-modified Y53C mutant of Aplysia AChBP in complex with acetylcholine
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / AMIDATION / CONFORMATIONAL FLEXIBILITY / CONOTOXIN / NEUROTOXINNICOTINIC / POSTSYNAPTIC NEUROTOXIN / RECEPTOR/TOXIN
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / membrane / identical protein binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETYLCHOLINE / PHOSPHATE ION / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBrams, M. / Gay, E.A. / Colon Saez, J. / Guskov, A. / van Elk, R. / van der Schors, R.C. / Peigneur, S. / Tytgat, J. / Strelkov, S.V. / Smit, A.B. ...Brams, M. / Gay, E.A. / Colon Saez, J. / Guskov, A. / van Elk, R. / van der Schors, R.C. / Peigneur, S. / Tytgat, J. / Strelkov, S.V. / Smit, A.B. / Yakel, J.L. / Ulens, C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures of a Cysteine-Modified Mutant in Loop D of Acetylcholine Binding Protein
Authors: Brams, M. / Gay, E.A. / Colon Saez, J. / Guskov, A. / Van Elk, R. / Van Der Schors, R.C. / Peigneur, S. / Tytgat, J. / Strelkov, S.V. / Smit, A.B. / Yakel, J.L. / Ulens, C.
History
DepositionNov 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Atomic model / Other / Version format compliance
Revision 1.2Feb 5, 2014Group: Refinement description
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,23239
Polymers123,3735
Non-polymers3,85934
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17400 Å2
ΔGint-81.2 kcal/mol
Surface area49890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.123, 119.405, 267.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.029, -0.004), (-0.024, 0.725, 0.689), (-0.017, 0.689, -0.725)
Vector: 52.963, 0.539, 0.403)

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Components

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Protein / Sugars , 2 types, 7 molecules ABCDE

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACHBP


Mass: 24674.639 Da / Num. of mol.: 5 / Fragment: RESIDUES 20-236 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 273 molecules

#2: Chemical
ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H16NO2 / Comment: neurotransmitter*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 72 TO CYS ENGINEERED RESIDUE IN CHAIN B, TYR 72 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, TYR 72 TO CYS ENGINEERED RESIDUE IN CHAIN B, TYR 72 TO CYS ENGINEERED RESIDUE IN CHAIN C, TYR 72 TO CYS ENGINEERED RESIDUE IN CHAIN D, TYR 72 TO CYS ENGINEERED RESIDUE IN CHAIN E, TYR 72 TO CYS
Nonpolymer detailsTHE MODIFIED RESIDUE S-METHYL-THIO-CYSTEINE (SCH) HAS BEEN GENERATED AT A SPECIFIC MUTATION SITE ...THE MODIFIED RESIDUE S-METHYL-THIO-CYSTEINE (SCH) HAS BEEN GENERATED AT A SPECIFIC MUTATION SITE TYR53 WHICH HAS BEEN MUTATED TO CYS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.18 % / Description: NONE
Crystal growDetails: 200 MM NH4(H2PO4), 100 MM TRIS PH 8.5 AND 50% MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→47.6 Å / Num. obs: 31966 / % possible obs: 92 % / Observed criterion σ(I): 1.9 / Redundancy: 5.9 % / Biso Wilson estimate: 50.49 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 77.5

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UZ6

2uz6


Resolution: 2.8→47.59 Å / Cor.coef. Fo:Fc: 0.9189 / Cor.coef. Fo:Fc free: 0.8814 / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS REPRESENTATION : RESTRAINT LSSR (-AUTONCS). IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=SCH NAG ACH CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM ...Details: NCS REPRESENTATION : RESTRAINT LSSR (-AUTONCS). IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=SCH NAG ACH CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=8552. NUMBER WITH APPROX DEFAULT DEFAULT CCP4 ATOM TYPE=168. NUMBER TREATED BY BAD NON-BONDED CONTACTS=5.
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 1630 5.1 %RANDOM
Rwork0.1729 ---
obs0.1753 31966 --
Displacement parametersBiso mean: 47.85 Å2
Baniso -1Baniso -2Baniso -3
1-13.2333 Å20 Å20 Å2
2---3.1512 Å20 Å2
3----10.0822 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 239 241 8725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018657HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0911818HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3879SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes242HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1204HARMONIC5
X-RAY DIFFRACTIONt_it8657HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1145SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9700SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.89 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2847 161 5.44 %
Rwork0.2366 2798 -
all0.2391 2959 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5482-0.02620.35191.2838-0.02871.3464-0.0951-0.08270.09450.04890.06940.13480.0336-0.20070.02570.06850.02380.009-0.1497-0.0341-0.1381-20.30513.374132.5961
21.38770.0445-0.07410.7446-0.12611.84180.0642-0.0878-0.12070.06690.0342-0.04780.30950.133-0.09840.20580.05310.0042-0.1942-0.0108-0.18750.2905-13.151937.2086
31.40470.0119-0.4551.63590.091.64370.0156-0.01450.1614-0.0037-0.00770.0616-0.3339-0.0391-0.00790.15580.0449-0.0323-0.2126-0.0341-0.1807-10.204127.25525.9094
41.2767-0.05290.09571.63020.66261.85520.0429-0.00910.10130.0078-0.057-0.0829-0.13030.10060.01410.119-0.1033-0.0048-0.1298-0.001-0.205216.479425.515826.3809
50.69490.27420.05711.753-0.02351.96190.0084-0.0775-0.05120.0496-0.0246-0.1945-0.11660.50230.0162-0.01010.0532-0.02680.0164-0.0083-0.196323.07060.572633.3805
60.47710.68650.07250.62160.4690.3916-0.00540.03250-0.00720.0443-0.048-0.04720.1104-0.03890.0963-0.04140.0046-0.05120.0679-0.03547.851110.009333.7012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A1-A208)
2X-RAY DIFFRACTION2(B1-B208)
3X-RAY DIFFRACTION3(C1-C208)
4X-RAY DIFFRACTION4(D1-D208)
5X-RAY DIFFRACTION5(E1-E208)
6X-RAY DIFFRACTION6(A1210-A1215, B1210-B1216, C1210-C1215, D1210-D1218, E1210-E1215)

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