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- PDB-3plc: Crystal structure of Beta-Cardiotoxin, a novel three-finger cardi... -

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Basic information

Entry
Database: PDB / ID: 3plc
TitleCrystal structure of Beta-Cardiotoxin, a novel three-finger cardiotoxin from the venom of Ophiophagus hannah
ComponentsBeta-cardiotoxin OH-27
KeywordsTOXIN / Beta-Cardiotoxin / Beta-sheet / Novel Cardiotoxin
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake cytotoxin, cobra-type / Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Beta-cardiotoxin CTX27
Similarity search - Component
Biological speciesOphiophagus hannah (king cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.41 Å
AuthorsRoy, A. / Qingxiang, S. / Kini, R.M. / Sivaraman, J.
CitationJournal: Protein Sci. / Year: 2019
Title: Identification of a alpha-helical molten globule intermediate and structural characterization of beta-cardiotoxin, an all beta-sheet protein isolated from the venom of Ophiophagus hannah (king cobra).
Authors: Roy, A. / Qingxiang, S. / Alex, C. / Rajagopalan, N. / Jobichen, C. / Sivaraman, J. / Kini, R.M.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 1, 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-cardiotoxin OH-27
B: Beta-cardiotoxin OH-27
C: Beta-cardiotoxin OH-27


Theoretical massNumber of molelcules
Total (without water)21,0943
Polymers21,0943
Non-polymers00
Water00
1
A: Beta-cardiotoxin OH-27


Theoretical massNumber of molelcules
Total (without water)7,0311
Polymers7,0311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-cardiotoxin OH-27


Theoretical massNumber of molelcules
Total (without water)7,0311
Polymers7,0311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-cardiotoxin OH-27


Theoretical massNumber of molelcules
Total (without water)7,0311
Polymers7,0311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.949, 58.949, 53.026
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 26
2114B1 - 26
3114C1 - 26
1214A36 - 70
2214B36 - 70
3214C36 - 70

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Components

#1: Protein Beta-cardiotoxin OH-27


Mass: 7031.463 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ophiophagus hannah (king cobra) / Tissue: venom gland / References: UniProt: Q69CK0
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: 2.52 Å3/Da / Density % sol: 51.22 % / Mosaicity: 1.195 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% (w/v) PEG 1500, Spermidine additive, pH 7, vapour diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker AXIOM 200 / Detector: CCD / Date: Nov 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.486
11-H-K, K, -L20.514
ReflectionResolution: 2.41→50.01 Å / Num. obs: 7999 / % possible obs: 99.6 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.137 / Χ2: 0.517 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.41-2.58.90.4847840.34196
2.5-2.611.10.4197860.3771100
2.6-2.7111.30.3388110.4181100
2.71-2.8611.30.2818020.471100
2.86-3.0411.30.2328010.4931100
3.04-3.2711.50.188100.5441100
3.27-3.611.40.1518040.5621100
3.6-4.1211.40.1278030.6111100
4.12-5.1911.20.1097890.6371100
5.19-5011.30.0948090.673199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KXI

1kxi


Resolution: 2.41→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.88 / WRfactor Rfree: 0.2626 / WRfactor Rwork: 0.2365 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7801 / SU B: 24.032 / SU ML: 0.219 / SU R Cruickshank DPI: 0.0975 / SU Rfree: 0.0587 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 787 9.9 %RANDOM
Rwork0.234 ---
obs0.2373 7983 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.47 Å2 / Biso mean: 45.967 Å2 / Biso min: 5.69 Å2
Baniso -1Baniso -2Baniso -3
1--9.93 Å20 Å20 Å2
2---9.93 Å20 Å2
3---19.86 Å2
Refinement stepCycle: LAST / Resolution: 2.41→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 0 0 1293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221319
X-RAY DIFFRACTIONr_angle_refined_deg1.8962.0321789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6755166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77525.94637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.53115261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.035156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022898
X-RAY DIFFRACTIONr_mcbond_it1.1691.5865
X-RAY DIFFRACTIONr_mcangle_it2.12321426
X-RAY DIFFRACTIONr_scbond_it2.1463454
X-RAY DIFFRACTIONr_scangle_it3.7124.5363
Refine LS restraints NCS

Ens-ID: 1 / Number: 398 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.370.5
2BMEDIUM POSITIONAL0.370.5
3CMEDIUM POSITIONAL0.370.5
1AMEDIUM THERMAL1.592
2BMEDIUM THERMAL1.882
3CMEDIUM THERMAL1.882
LS refinement shellResolution: 2.406→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 68 -
Rwork0.252 510 -
all-578 -
obs--95.7 %
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)
13.29571.04620.18952.75540.44323.33120.0705-0.12470.12860.048-0.09060.04370.0652-0.18310.020.2568-0.02540.00820.23340.02490.0948-6.4283.753-0.086
25.1601-0.1412-0.4922.33951.70053.5432-0.06280.02480.017-0.1380.03980.1611-0.20940.08490.0230.271-0.0187-0.01180.21940.0570.120824.264-21.379-11.979
32.0927-0.13770.34671.1095-0.06842.7637-0.07720.0888-0.0764-0.187-0.0428-0.02390.0732-0.09990.11990.19010.0038-0.00640.2640.00380.10386.582-34.934-20.319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 62
2X-RAY DIFFRACTION2B1 - 62
3X-RAY DIFFRACTION3C1 - 62

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