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- PDB-1i9b: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) -

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Basic information

Entry
Database: PDB / ID: 1i9b
TitleX-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP)
ComponentsACETYLCHOLINE BINDING PROTEIN
KeywordsLIGAND BINDING PROTEIN / pentamer / igg fold
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / synapse / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsBrejc, K. / van Dijk, W.J. / Klaassen, R. / Schuurmans, M. / van der Oost, J. / Smit, A.B. / Sixma, T.K.
Citation
Journal: Nature / Year: 2001
Title: Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors.
Authors: Brejc, K. / van Dijk, W.J. / Klaassen, R.V. / Schuurmans, M. / van Der Oost, J. / Smit, A.B. / Sixma, T.K.
#1: Journal: Nature / Year: 2001
Title: A glia-derived acetylcholine-binding protein that modulates synaptic transmission
Authors: Smit, A.B. / Syed, N.I. / Schaap, D. / van Minnen, J. / Klumperman, J. / Kits, K.S. / Lodder, H. / van der Schors, R.C. / van Elk, R. / Sorgedrager, B. / Brejc, K. / Sixma, T.K. / Geraerts, W.P.M.
History
DepositionMar 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE SEQUENCE FOR THE PROTEIN IS NOT YET DEPOSITED IN THE SEQUENCE DATABASE. THE EXPRESSED ...SEQUENCE THE SEQUENCE FOR THE PROTEIN IS NOT YET DEPOSITED IN THE SEQUENCE DATABASE. THE EXPRESSED PROTEIN HAS A MUATAION AT RESIDUE 1: L1F. RESIDUES -6 TO 0 (EAEAYVE) ARE CLONING ARTIFACTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINE BINDING PROTEIN
B: ACETYLCHOLINE BINDING PROTEIN
C: ACETYLCHOLINE BINDING PROTEIN
D: ACETYLCHOLINE BINDING PROTEIN
E: ACETYLCHOLINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,95418
Polymers123,4425
Non-polymers1,51213
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16070 Å2
ΔGint-75 kcal/mol
Surface area42550 Å2
MethodPISA
2
A: ACETYLCHOLINE BINDING PROTEIN
B: ACETYLCHOLINE BINDING PROTEIN
C: ACETYLCHOLINE BINDING PROTEIN
D: ACETYLCHOLINE BINDING PROTEIN
E: ACETYLCHOLINE BINDING PROTEIN
hetero molecules

A: ACETYLCHOLINE BINDING PROTEIN
B: ACETYLCHOLINE BINDING PROTEIN
C: ACETYLCHOLINE BINDING PROTEIN
D: ACETYLCHOLINE BINDING PROTEIN
E: ACETYLCHOLINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,90836
Polymers246,88310
Non-polymers3,02426
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area35990 Å2
ΔGint-221 kcal/mol
Surface area81680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.660, 141.660, 120.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11E-310-

CA

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Components

#1: Protein
ACETYLCHOLINE BINDING PROTEIN / ACHBP


Mass: 24688.342 Da / Num. of mol.: 5 / Mutation: L1F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS 115 / References: UniProt: P58154
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, CALCIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
211.5 %(w/v)PEG40001reservoir
3100 mMHEPES1reservoir
4150 mM1reservoirCaCl2
50.02 %(w/v)1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.943 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 2.7→44 Å / Num. all: 34483 / Num. obs: 34483 / % possible obs: 97.8 % / Observed criterion σ(I): 2.3 / Redundancy: 6.5 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 2515375.59 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1558 4.6 %SHELLS
Rwork0.26 ---
obs0.26 33535 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.86 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 61.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.49 Å20 Å20 Å2
2--5.49 Å20 Å2
3----10.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8195 0 85 19 8299
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.281.5
X-RAY DIFFRACTIONc_mcangle_it6.362
X-RAY DIFFRACTIONc_scbond_it6.312
X-RAY DIFFRACTIONc_scangle_it8.432.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 244 4.5 %
Rwork0.4 5183 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4hep_xplor_par.txt
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / σ(F): 0 / % reflection Rfree: 4.6 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.434 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.4

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