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- PDB-2x00: CRYSTAL STRUCTURE OF A-ACHBP IN COMPLEX WITH GYMNODIMINE A -

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Basic information

Entry
Database: PDB / ID: 2x00
TitleCRYSTAL STRUCTURE OF A-ACHBP IN COMPLEX WITH GYMNODIMINE A
Components(SOLUBLE ACETYLCHOLINE RECEPTOR) x 2
KeywordsRECEPTOR / PHYCOTOXIN / TOXIN / ACETYLCHOLINE BINDING PROTEIN
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
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
GYMNODIMINE A / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBourne, Y. / Radic, Z. / Araoz, R. / Talley, T.T. / Benoit, E. / Servent, D. / Taylor, P. / Molgo, J. / Marchot, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Determinants in Phycotoxins and Achbp Conferring High Affinity Binding and Nicotinic Achr Antagonism.
Authors: Bourne, Y. / Radic, Z. / Araoz, R. / Talley, T.T. / Benoit, E. / Servent, D. / Taylor, P. / Molgo, J. / Marchot, P.
History
DepositionDec 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)132,25910
Polymers129,7105
Non-polymers2,5495
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-69.8 kcal/mol
Surface area44830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.430, 124.320, 130.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR


Mass: 25967.832 Da / Num. of mol.: 4 / Fragment: RESIDUES 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell line: SENSORY CELL / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) / Variant (production host): GNT1- / References: UniProt: Q8WSF8
#2: Protein SOLUBLE ACETYLCHOLINE RECEPTOR


Mass: 25838.652 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell line: SENSORY CELL / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) / Variant (production host): GNT1- / References: UniProt: Q8WSF8
#3: Chemical
ChemComp-GYN / GYMNODIMINE A


Mass: 509.720 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H47NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFLAG EPITOPE DYKDDDDKL AT N-TER OF EACH SUBUNIT

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5
Details: 27-30% PEG-400, 0.1 M HEPES, PH 7.5-7.7, 0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 47713 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.9 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYR

2byr


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.178 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23503 2391 5 %RANDOM
Rwork0.18034 ---
obs0.18305 45448 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2---1.87 Å2-0 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8506 0 185 392 9083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229021
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.97612344
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31751087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3724.356427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.695151442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3151555
X-RAY DIFFRACTIONr_chiral_restr0.0770.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216935
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4161.55394
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81528821
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23533627
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0574.53512
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 169 -
Rwork0.22 3218 -
obs--100 %
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)
11.0489-0.13250.23781.2433-0.14681.0383-0.0554-0.08690.07380.0870.004-0.111-0.00470.01450.05130.0188-0.01060.00160.0321-0.02040.029418.274514.40420.8308
21.04250.1482-0.11691.0592-0.28271.5678-0.037-0.0633-0.11420.0488-0.0141-0.25930.0180.06770.05110.01540.0183-0.01020.030.00090.079521.2177-11.81824.5929
31.4231-0.1735-0.03470.99350.07341.1426-0.0164-0.1373-0.15690.07580.02540.06540.0307-0.0089-0.00910.03240.00460.01320.01590.00990.0433-2.6738-22.66663.651
41.2538-0.06940.04131.63170.00291.192-0.0483-0.12540.04810.07580.01390.1877-0.043-0.05990.03440.00690.00560.00740.0223-0.01390.0349-20.673-3.5411-1.094
51.1788-0.09120.10041.24490.29750.8741-0.0269-0.07130.20860.07950.02490.09110.0217-0.00450.0020.02550.00360.0040.0059-0.01220.0505-7.970419.8316-3.2689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 208
2X-RAY DIFFRACTION2B-5 - 209
3X-RAY DIFFRACTION3C-5 - 207
4X-RAY DIFFRACTION4D-3 - 208
5X-RAY DIFFRACTION5E-3 - 208

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