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- PDB-1xt3: Structure Basis of Venom Citrate-Dependent Heparin Sulfate-Mediat... -

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Basic information

Entry
Database: PDB / ID: 1xt3
TitleStructure Basis of Venom Citrate-Dependent Heparin Sulfate-Mediated Cell Surface Retention of Cobra Cardiotoxin A3
ComponentsCytotoxin 3Cytotoxicity
KeywordsTOXIN / CTX-3 / heparin / citrate
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 three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Cytotoxin 3
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLee, S.-C. / Guan, H.-H. / Wang, C.-H. / Huang, W.-N. / Chen, C.-J. / Wu, W.-G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural basis of citrate-dependent and heparan sulfate-mediated cell surface retention of cobra cardiotoxin A3
Authors: Lee, S.-C. / Guan, H.-H. / Wang, C.-H. / Huang, W.-N. / Tjong, S.-C. / Chen, C.-J. / Wu, W.-G.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxin 3
B: Cytotoxin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4594
Polymers13,5172
Non-polymers1,9432
Water18010
1
A: Cytotoxin 3
hetero molecules

B: Cytotoxin 3


Theoretical massNumber of molelcules
Total (without water)15,4594
Polymers13,5172
Non-polymers1,9432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
Buried area2780 Å2
ΔGint-1 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.903, 59.447, 98.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cytotoxin 3 / Cytotoxicity / Cardiotoxin 3 / CTX-3 / Cardiotoxin analog III / CTX III


Mass: 6758.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: P60301
#2: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1750.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.893 Å3/Da / Density % sol: 35.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, isopropanol, trisodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.1274 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1274 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 5051 / Num. obs: 4889 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.038
Reflection shellResolution: 2.4→2.48 Å / % possible all: 83.6

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Processing

Software
NameClassification
XDSdata scaling
SCALEPACKdata scaling
CNSrefinement
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 245 RANDOM
Rwork0.227 --
all0.242 5051 -
obs0.231 4889 -
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 118 10 1058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.17

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