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- PDB-2bj0: Crystal Structure of AChBP from Bulinus truncatus revals the cons... -

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Basic information

Entry
Database: PDB / ID: 2bj0
TitleCrystal Structure of AChBP from Bulinus truncatus revals the conserved structural scaffold and sites of variation in nicotinic acetylcholine receptors
ComponentsACETYLCHOLINE-BINDING PROTEIN
KeywordsGLYCOPROTEIN / GLYCPROTEIN / IGG FOLD / IMMUNOGLOBULIN DOMAIN / PENTAMER
Function / homologyAcetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Distorted Sandwich / Mainly Beta
Function and homology information
Biological speciesBULINUS TRUNCATUS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCelie, P.H.N. / Klaassen, R.V. / Van Rossum-Fikkert, S.E. / Van Elk, R. / Van Nierop, P. / Smit, A.B. / Sixma, T.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Acetylcholine-Binding Protein from Bulinus Truncatus Reveals the Conserved Structural Scaffold and Sites of Variation in Nicotinic Acetylcholine Receptors.
Authors: Celie, P.H.N. / Klaassen, R.V. / Van Rossum-Fikkert, S.E. / Van Elk, R. / Van Nierop, P. / Smit, A.B. / Sixma, T.K.
History
DepositionJan 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)115,4309
Polymers114,5445
Non-polymers8854
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.945, 219.018, 166.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-2001-

HOH

21E-2006-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.29637, 0.95469, -0.02704), (-0.95345, 0.2941, -0.06662), (-0.05565, 0.04552, 0.99741)-47.94117, 95.66893, -1.66347
2given(-0.79796, 0.59583, -0.09083), (-0.59389, -0.80299, -0.0501), (-0.10279, 0.01397, 0.99461)25.96479, 168.17766, 2.90733
3given(-0.79442, -0.59966, -0.09641), (0.60074, -0.79918, 0.02067), (-0.08944, -0.04149, 0.99513)120.90076, 119.18094, 6.86199
4given(0.31653, -0.94815, -0.02878), (0.94751, 0.31458, 0.05707), (-0.04506, -0.04533, 0.99796)102.63296, 15.30942, 5.23801

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Components

#1: Protein
ACETYLCHOLINE-BINDING PROTEIN


Mass: 22908.893 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: CAPS BUFFER MOLECULE IS COCRYSTALLIZED IN THE LIGAND BINDING-SITE. CAPS COULD BE BUILT IN 4 OUT OF 5 BINDING SITES WITHIN THE PENTAMER
Source: (gene. exp.) BULINUS TRUNCATUS (invertebrata) / Cell: GLIAL / Plasmid: PFASTBACI / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
#2: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsACHBP FROM BULINUS TRUNCATUS CONTAINS SIGNAL SEQUENCE (MAELRGIILL LCTIAFHVSH G) THAT PRECEDES ...ACHBP FROM BULINUS TRUNCATUS CONTAINS SIGNAL SEQUENCE (MAELRGIILL LCTIAFHVSH G) THAT PRECEDES RESIDUE GLN 1 AND IS REMOVED UPON SECRETION. THIS SIGNAL SEQUENCE IS PRESENT IN THE GENBANK DATAFILE. THE UNIPROT ID WILL BE REFERENCED AS SOON AS IT IS AVAILABLE.

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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: 2.9 Å3/Da / Density % sol: 57.7 %
Crystal growpH: 10.5
Details: 0.1 M CAPS PH10.5, 0.2 M LITHIUMSULFATE, 2 M AMMONIUM SULFATE, pH 10.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2→44.72 Å / Num. obs: 93560 / % possible obs: 98 % / Observed criterion σ(I): 1.7 / Redundancy: 5.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I9B

1i9b


Resolution: 2→12 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.748 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4645 5 %RANDOM
Rwork0.21 ---
obs0.212 88439 97.7 %-
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: 34.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å20 Å2
2---2.11 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8050 0 56 424 8530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.94911350
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00851016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10725.163368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.954151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3741535
X-RAY DIFFRACTIONr_chiral_restr0.1040.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026183
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23485
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2494
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1121.55240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84628360
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.47833565
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9614.52990
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 244
Rwork0.292 5422

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