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- PDB-4iye: Crystal structure of AdTx1 (rho-Da1a) from eastern green mamba (D... -

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Basic information

Entry
Database: PDB / ID: 4iye
TitleCrystal structure of AdTx1 (rho-Da1a) from eastern green mamba (Dendroaspis angusticeps)
ComponentsToxin AdTx1
KeywordsTOXIN / Snake three-finger toxin family / Type A muscarinic toxin subfamily / Allosteric antagonist of the alpha-1A adrenergic receptor (ADRA1A) / Acts as a relaxant of smooth muscle / alpha-1A adrenergic receptor / g-rhoDa1a K34A / Expressed by the venom gland
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Toxin AdTx1
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsStura, E.A. / Vera, L. / Maiga, A.A. / Marchetti, C. / Lorphelin, A. / Bellanger, L. / Servant, D. / Gilles, N.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization of recombinant green mamba rho-Da1a toxin during a lyophilization procedure and its structure determination.
Authors: Maiga, A. / Vera, L. / Marchetti, C. / Lorphelin, A. / Bellanger, L. / Mourier, G. / Servent, D. / Gilles, N. / Stura, E.A.
#1: Journal: Acta Crystallogr.,Sect.F
Title: Crystallization of Da1a from Green mamba venom during lyophilization
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin AdTx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5754
Polymers7,3001
Non-polymers2743
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.370, 37.370, 66.050
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 Toxin AdTx1 / Rho-EPTX-Da1a


Mass: 7300.272 Da / Num. of mol.: 1 / Fragment: Rho-Da1a / Mutation: K34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis angusticeps (eastern green mamba)
Strain: angusticeps / Organ: Venom gland
Plasmid details: The synthetic gene corresponds to the ENLYFQG-rho-Da1a protein flanked by the attB1 and attB2 sequences
Plasmid: pENTRE plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P85092
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 1.82 Å3/Da / Density % sol: 32.56 %
Crystal growTemperature: 273 K / Method: lyophilization / pH: 8
Details: Crystallization during lyophilization due to increased concentration and low temperature. Cryoconditions: 27% PEG8K, 15% MPEG550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, Lyophilization, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.95→32.36 Å / Num. all: 4193 / Num. obs: 3937 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 8.44 % / Biso Wilson estimate: 25.325 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.16 / Net I/σ(I): 11.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.95-2.072.891.0881.126600.94769.1
2.07-2.2140.691.966200.60392.1
2.21-2.396.160.583.155710.52599.5
2.39-2.6110.640.4386.075330.425100
2.61-2.9211.790.3169.174990.303100
2.92-3.3711.610.17515.544390.166100
3.37-4.1111.390.08926.843780.083100
4.11-5.7711.040.06632.972970.06100
5.77-32.369.670.0635.851960.055100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF4 without loop 1 tip

1ff4


Resolution: 1.951→32.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.031 / SU ML: 0.156 / Isotropic thermal model: Anisotropic TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25188 197 5 %RANDOM
Rwork0.17033 ---
all0.17545 3937 --
obs0.17445 3738 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.704 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å21.63 Å2-0 Å2
2--1.63 Å2-0 Å2
3----5.28 Å2
Refinement stepCycle: LAST / Resolution: 1.951→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms505 0 18 70 593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019540
X-RAY DIFFRACTIONr_bond_other_d0.0020.02498
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.977729
X-RAY DIFFRACTIONr_angle_other_deg1.2333.0141150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.225567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03224.34823
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4621585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.449153
X-RAY DIFFRACTIONr_chiral_restr0.080.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021595
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02112
X-RAY DIFFRACTIONr_rigid_bond_restr5.0423522
X-RAY DIFFRACTIONr_sphericity_bonded12.7565507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.951-2.0020.5190.2917217260.33
2.002-2.0550.15110.2620773.15
2.055-2.1150.41120.2323288.09
2.115-2.1780.29130.2324092.67
2.178-2.250.18130.225998.91
2.25-2.3260.31140.225599.63
2.326-2.4140.46110.19225100
2.414-2.5090.36130.17241100
2.509-2.6380.19120.17222100
2.638-2.7460.22110.17206100
2.746-2.9110.24110.16213100
2.911-3.0650.14100.13191100
3.065-3.2910.21100.13191100
3.291-3.5290.2790.11165100
3.529-3.8730.1580.11162100
3.873-4.2910.280.11148100
4.291-4.9340.2570.12133100
4.934-5.9130.2460.14115100
5.913-7.8880.1850.1799100
7.888-32.360.0840.1762100
Refinement TLS params.Method: refined / Origin x: -16.1157 Å / Origin y: 12.5129 Å / Origin z: 13.2222 Å
111213212223313233
T0.0013 Å20.0012 Å20.002 Å2-0.0015 Å20.0033 Å2--0.0507 Å2
L0.0376 °20.0618 °2-0.0143 °2-0.136 °20.041 °2--0.1505 °2
S-0.006 Å °-0.0025 Å °-0.0061 Å °-0.0045 Å °0.0022 Å °0.008 Å °0.0108 Å °0.0142 Å °0.0038 Å °

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