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- PDB-1qm7: X-ray structure of a three-fingered chimeric protein, stability o... -

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Basic information

Entry
Database: PDB / ID: 1qm7
TitleX-ray structure of a three-fingered chimeric protein, stability of a structural scaffold
ComponentsR-CHII
KeywordsTOXIN / STABILITY OF A STRUCTURAL SCAFFOLD
Function / homologyCD59 / CD59 / Ribbon / Mainly Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLe Du, M.H. / Ricciardi, A. / Khayati, M. / Menez, R. / Boulain, J.C. / Menez, A. / Ducancel, F.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Stability of a Structural Scaffold Upon Activity Transfer : X-Ray Structure of a Three Fingers Chimeric Protein.
Authors: Le Du, M.H. / Ricciardi, A. / Khayati, M. / Menez, R. / Boulain, J.C. / Menez, A. / Ducancel, F.
History
DepositionSep 21, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0May 1, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R-CHII


Theoretical massNumber of molelcules
Total (without water)6,6951
Polymers6,6951
Non-polymers00
Water90150
1
A: R-CHII

A: R-CHII


Theoretical massNumber of molelcules
Total (without water)13,3902
Polymers13,3902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1160 Å2
ΔGint-6 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.480, 58.480, 62.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein R-CHII


Mass: 6694.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FULLY ENGINEERED PROTEIN CONTAINING 41% RESIDUES FROM FASCICULIN 2,25% FROM ALPHA-TOXIN, 34% CONSERVED BETWEEN THE TWO NATURAL TOXINS
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Gene: SYNTHETIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE MOLECULE STUDIED HERE IS A SYNTHETIC CHIMERIC PROTEIN FULLY ENGINEERED PROTEIN CONTAINING 41% ...THE MOLECULE STUDIED HERE IS A SYNTHETIC CHIMERIC PROTEIN FULLY ENGINEERED PROTEIN CONTAINING 41% RESIDUES FROM FASCICULIN 2, 25% FROM ALPHA-TOXIN, 34% CONSERVED BETWEEN THE TWO NATURAL SNAKE VENOMS, MOLECULE: ACETYLCHOLINESTERASE TOXIN F-VII SYNONYM: FASCICULINS II ORGANISM_SCIENTIFIC: DENDROASPIS ANGUSTICEPS ORGANISM_COMMON: EASTERN GREEN MAMBA DBREF: SWS TXF7_DENAN P01403 IDENTITY (FASTA): 75.806% AND MOLECULE: SHORT NEUROTOXIN 1 SYNONYM: NEUROTOXIN ALPHA ORGANISM_SCIENTIFIC: NAJA PALLIDA (NIGRICOLLIS) ORGANISM_COMMON: RED SPITTING COBRA (BLACK-NECKED SPITTING COBRA) DBREF SWS NXS1_NAJPA P01426 IDENTITY (FASTA): 58.621% ALIGNMENTS: NXS1_NAJPA LECHNQQSSQPPTTKTCPGETNCYKKVWRDHRGTIIERGCGCP : :::::::::: : :::::: 1QM7 TMCYSHTTTSRAILTNCPGETNCYKKSRRHPPKMVLGRGCGCP ::::::::::::::::: :: :: :::::::::::::::::: TXF7_DENAN TMCYSHTTTSRAILTNCG-ENSCYRKSRRHPPKMVLGRGCGCP NXS1_NAJPA TVKPGIKLNCCTTDKCNNY :: :::::::::::::: 1QM7 TVAPGIKLNCCTT-DKCNY ::: ::::: TXF7_DENAN PGDDYLEVKCCTSPDKCNY

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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: 4.42 Å3/Da / Density % sol: 72 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal
*PLUS
Density % sol: 72.2 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 7312 / % possible obs: 97 % / Redundancy: 3 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.063 / Net I/σ(I): 22.3
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.538 / % possible all: 99.5
Reflection
*PLUS
Rmerge(I) obs: 0.063 / Biso Wilson estimate: 37.9 Å2
Reflection shell
*PLUS
% possible obs: 41 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FASCICULIN 2

Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 340 5 %RANDOM
Rwork0.202 ---
obs-7312 96 %-
Displacement parametersBiso mean: 57 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms458 0 0 50 508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.023
X-RAY DIFFRACTIONp_angle_d2.866
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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