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- PDB-2vlw: Crystal structure of the muscarinic toxin MT7 diiodoTYR51 derivative. -

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Basic information

Entry
Database: PDB / ID: 2vlw
TitleCrystal structure of the muscarinic toxin MT7 diiodoTYR51 derivative.
ComponentsMUSCARINIC M1-TOXIN1
KeywordsTOXIN / ACETYLCHOLINE RECEPTOR INHIBITOR / GREEN MAMBA SNAKE TOXIN / HM1 MUSCARINIC RECEPTOR / SECRETED / NEUROTOXIN / DIIODOTYROSINE / MUSCARINIC TOXIN / POSTSYNAPTIC NEUROTOXIN
Function / homology
Function and homology information


receptor antagonist activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Muscarinic toxin 7
Similarity search - Component
Biological speciesDENDROASPIS ANGUSTICEPS (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsMenez, R. / Granata, V. / Mourier, G. / Fruchart-Gaillard, C. / Menez, A. / Servant, D. / Stura, E.A.
Citation
Journal: Mol.Pharmacol. / Year: 2008
Title: Different Interactions between Mt7 Toxin and the Human Muscarinic M1 Receptor in its Free and N-Methylscopolamine-Occupied States.
Authors: Fruchart-Gaillard, C. / Mourier, G. / Marquer, C. / Stura, E. / Birdsall, N.J.M. / Servent, D.
#1: Journal: To be Published
Title: Comparison of the Structures of Two Muscarinic Toxins from Green Mamba Venom
Authors: Menez, R. / Granata, V. / Mourier, G. / Ledu, M.H. / Servant, D. / Menez, A. / Stura, E.A.
History
DepositionJan 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2008Provider: 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 / 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_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 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: MUSCARINIC M1-TOXIN1
B: MUSCARINIC M1-TOXIN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7345
Polymers15,4832
Non-polymers2513
Water3,117173
1
A: MUSCARINIC M1-TOXIN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8963
Polymers7,7411
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MUSCARINIC M1-TOXIN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8372
Polymers7,7411
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.766, 56.577, 45.308
Angle α, β, γ (deg.)90.00, 95.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99997, 0.00469, 0.0061), (-0.00468, -0.99999, 0.00067), (0.0061, 0.00064, 0.99998)
Vector: -13.38899, -22.16051, 0.04153)

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Components

#1: Protein MUSCARINIC M1-TOXIN1 / M1-TOXIN / MUSCARINIC TOXIN 7 / MT7 / MT-7 / MUSCARINIC SNAKE TOXIN


Mass: 7741.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICAL PEPTIDE SYNTHESIS ACCORDING TO SEQUENCE.
Source: (synth.) DENDROASPIS ANGUSTICEPS (eastern green mamba)
References: UniProt: Q8QGR0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSULFATE ION (SO4): SO4 FROM CRYSTALLIZATION PRECIPITANT OR CRYOSALT. ACETATE ION (ACT): ACETATE ...SULFATE ION (SO4): SO4 FROM CRYSTALLIZATION PRECIPITANT OR CRYOSALT. ACETATE ION (ACT): ACETATE FROM PROTEIN BUFFER. 3,5-DIIODOTYROSINE (TYI): 3,5-DIIODOTYROSINE INTRODUCED BY CHEMICAL SYNTHESIS
Sequence detailsY51 IS DIIODINATED

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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: 2.1 Å3/Da / Density % sol: 41.9 % / Description: NONE
Crystal growpH: 5.5
Details: 1.25M AMMONIUM SULFATE, 90MM SODIUM CITRATE, 10% 4-METHYL PENTANEDIOL, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.937801
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 16, 2005 / Details: MIRRORS
RadiationMonochromator: CHANNEL-CUT SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937801 Å / Relative weight: 1
ReflectionResolution: 1.39→45.13 Å / Num. obs: 24835 / % possible obs: 95.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKLdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF4

1ff4


Resolution: 1.39→45.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.217 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1309 5 %RANDOM
Rwork0.199 ---
obs0.2 24835 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.17 Å2
2---0.7 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.39→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 14 173 1229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221087
X-RAY DIFFRACTIONr_bond_other_d0.0020.02893
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9781479
X-RAY DIFFRACTIONr_angle_other_deg0.99432100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0765128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8523.7548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34115176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.844158
X-RAY DIFFRACTIONr_chiral_restr0.2850.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021194
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02222
X-RAY DIFFRACTIONr_nbd_refined0.2180.2200
X-RAY DIFFRACTIONr_nbd_other0.1980.2906
X-RAY DIFFRACTIONr_nbtor_refined0.190.2515
X-RAY DIFFRACTIONr_nbtor_other0.0930.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4140.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3970.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.5659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82221060
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9193502
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9714.5419
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: 1.39→1.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 92
Rwork0.337 1434

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