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- PDB-4om5: Crystal structure of CTX A4 from Taiwan Cobra (Naja naja atra) -

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Basic information

Entry
Database: PDB / ID: 4om5
TitleCrystal structure of CTX A4 from Taiwan Cobra (Naja naja atra)
ComponentsCytotoxin 4
KeywordsTOXIN / Five beta sheets / three functional loops / endocytosis / heparin / heparan sulfate
Function / homology
Function and homology information


other organism cell membrane / protein kinase inhibitor activity / 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: 2.55 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 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxin 4
B: Cytotoxin 4
C: Cytotoxin 4
D: Cytotoxin 4


Theoretical massNumber of molelcules
Total (without water)27,2174
Polymers27,2174
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.933, 72.933, 249.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

21C-119-

HOH

DetailsThe biological assembly is an oligomer.

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Components

#1: Protein
Cytotoxin 4 / Cardiotoxin analog IV / CTX IV / Cardiotoxin-A4 / CTX-4 / CTX-A4


Mass: 6804.278 Da / Num. of mol.: 4 / Fragment: UNP residues 22-81 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / Secretion: venom / References: UniProt: P01443
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.3 M ammonium sulfate, 100 mM Tris-HCl, 200 mM lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 4, 2009
RadiationMonochromator: 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: 2.55→50 Å / Num. all: 13697 / Num. obs: 13697 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 41.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.55-2.6441.80.9061100
2.64-2.7542.60.6371100
2.75-2.8742.50.4821100
2.87-3.0242.60.3331100
3.02-3.2142.50.2341100
3.21-3.4642.30.1611100
3.46-3.8141.90.1171100
3.81-4.3641.20.0991100
4.36-5.49390.11100
5.49-5035.50.072199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→31.05 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.426 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26235 675 5 %RANDOM
Rwork0.21492 ---
obs0.21724 12947 99.89 %-
all-13638 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.15 Å20 Å2
2--0.15 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.55→31.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 0 75 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021920
X-RAY DIFFRACTIONr_bond_other_d0.0030.021952
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9972596
X-RAY DIFFRACTIONr_angle_other_deg0.8663.0144472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8885236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.15723.12564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2281512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
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_it1.5591.957956
X-RAY DIFFRACTIONr_mcbond_other1.5581.956955
X-RAY DIFFRACTIONr_mcangle_it2.6082.9311188
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9312.058963
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: 2.552→2.618 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 44 -
Rwork0.298 932 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.26060.62670.11660.96210.58512.50870.1605-0.0118-0.05350.1568-0.2605-0.04860.1060.21170.10.3037-0.05890.00790.19180.00290.154825.27022.170816.3539
20.8423-0.17310.85812.41961.62872.436-0.10770.0323-0.0047-0.33360.0649-0.0076-0.38640.28890.04280.4088-0.14750.02190.22920.03360.098630.493622.03184.2796
30.98690.1083-0.01530.94260.46852.1520.25140.0505-0.14130.09-0.070.07280.1998-0.1401-0.18140.2635-0.0415-0.0430.15380.01210.2137.7772-7.89231.985
41.6118-0.36551.2731.88461.15872.33440.1419-0.2434-0.0563-0.0476-0.27270.4140.1421-0.24910.13080.1827-0.0893-0.0280.2855-0.15580.389612.601625.678422.629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 60
2X-RAY DIFFRACTION2B1 - 60
3X-RAY DIFFRACTION3C1 - 60
4X-RAY DIFFRACTION4D1 - 60

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