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- PDB-4om4: Crystal structure of CTX A2 from Taiwan Cobra (Naja naja atra) -

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Basic information

Entry
Database: PDB / ID: 4om4
TitleCrystal structure of CTX A2 from Taiwan Cobra (Naja naja atra)
ComponentsCytotoxin 2
KeywordsTOXIN / Five beta sheets / three functional loops / endocytosis / heparin / heparan sulfate
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / 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
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsLin, C.C. / Chang, C.I. / Wu, W.G.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Endocytotic Routes of Cobra Cardiotoxins Depend on Spatial Distribution of Positively Charged and Hydrophobic Domains to Target Distinct Types of Sulfated Glycoconjugates on Cell Surface.
Authors: Lee, S.C. / Lin, C.C. / Wang, C.H. / Wu, P.L. / Huang, H.W. / Chang, C.I. / Wu, W.G.
History
DepositionJan 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxin 2
B: Cytotoxin 2
C: Cytotoxin 2
D: Cytotoxin 2
E: Cytotoxin 2


Theoretical massNumber of molelcules
Total (without water)33,8015
Polymers33,8015
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.412, 107.412, 100.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-104-

HOH

DetailsThe biological assembly is an oligomer.

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Components

#1: Protein
Cytotoxin 2 / CX2 / Cardiotoxin 1A / Cardiotoxin analog II / CTX II / Cardiotoxin-A2 / CTX-2 / CTX-A2 / CTX2


Mass: 6760.242 Da / Num. of mol.: 5 / Fragment: UNP residues 22-81 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / Secretion: venom / References: UniProt: P01442
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 4.28 Å3/Da / Density % sol: 71.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 5.5 M ammonium nitrate, 0.1 M Bis-Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2009
RadiationMonochromator: LN2-cooled, fixed-exit double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→30 Å / Num. all: 15886 / Num. obs: 15865 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.74-2.84150.4941100
2.84-2.9515.70.381100
2.95-3.09160.2941100
3.09-3.2516.10.1811100
3.25-3.45160.1391100
3.45-3.72160.1031100
3.72-4.0915.90.0811100
4.09-4.6815.70.0641100
4.68-5.8915.40.0711100
5.89-3013.90.059199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BHI

2bhi


Resolution: 2.74→25.62 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.183 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 792 5 %RANDOM
Rwork0.1966 ---
obs0.19979 15030 99.58 %-
all-15886 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.846 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å2-0 Å2
2---2.31 Å20 Å2
3---4.62 Å2
Refinement stepCycle: LAST / Resolution: 2.74→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 0 92 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022385
X-RAY DIFFRACTIONr_bond_other_d0.0030.022430
X-RAY DIFFRACTIONr_angle_refined_deg1.9142.0033230
X-RAY DIFFRACTIONr_angle_other_deg0.8773.0145575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7435295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.632475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.12915455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8471510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3684.2611195
X-RAY DIFFRACTIONr_mcbond_other3.364.261194
X-RAY DIFFRACTIONr_mcangle_it5.1526.3841485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7464.6311189
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.745→2.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 52 -
Rwork0.308 1063 -
obs--96.79 %

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