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- PDB-1tgx: X-RAY STRUCTURE AT 1.55 A OF TOXIN GAMMA, A CARDIOTOXIN FROM NAJA... -

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Basic information

Entry
Database: PDB / ID: 1tgx
TitleX-RAY STRUCTURE AT 1.55 A OF TOXIN GAMMA, A CARDIOTOXIN FROM NAJA NIGRICOLLIS VENOM. CRYSTAL PACKING REVEALS A MODEL FOR INSERTION INTO MEMBRANES
ComponentsGAMMA-CARDIOTOXIN
KeywordsCYTOTOXIN
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
Biological speciesNaja nigricollis (spitting cobra)
MethodX-RAY DIFFRACTION / Resolution: 1.55 Å
AuthorsBilwes, A. / Rees, B. / Moras, D.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: X-ray structure at 1.55 A of toxin gamma, a cardiotoxin from Naja nigricollis venom. Crystal packing reveals a model for insertion into membranes.
Authors: Bilwes, A. / Rees, B. / Moras, D. / Menez, R. / Menez, A.
History
DepositionNov 24, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMA-CARDIOTOXIN
B: GAMMA-CARDIOTOXIN
C: GAMMA-CARDIOTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,01217
Polymers20,5153
Non-polymers49614
Water2,954164
1
B: GAMMA-CARDIOTOXIN
hetero molecules

B: GAMMA-CARDIOTOXIN
hetero molecules

A: GAMMA-CARDIOTOXIN
C: GAMMA-CARDIOTOXIN
hetero molecules

A: GAMMA-CARDIOTOXIN
C: GAMMA-CARDIOTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,02334
Polymers41,0316
Non-polymers99328
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8160 Å2
ΔGint-276 kcal/mol
Surface area21100 Å2
MethodPISA
2
A: GAMMA-CARDIOTOXIN
hetero molecules

A: GAMMA-CARDIOTOXIN
hetero molecules

B: GAMMA-CARDIOTOXIN
hetero molecules

B: GAMMA-CARDIOTOXIN
hetero molecules

C: GAMMA-CARDIOTOXIN
hetero molecules

C: GAMMA-CARDIOTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,02334
Polymers41,0316
Non-polymers99328
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_556x+1/2,y+1/2,z+11
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation3_454x-1/2,y+1/2,z-11
crystal symmetry operation4_657-x+3/2,y+1/2,-z+21
Buried area6690 Å2
ΔGint-261 kcal/mol
Surface area22940 Å2
MethodPISA
3
A: GAMMA-CARDIOTOXIN
hetero molecules

A: GAMMA-CARDIOTOXIN
hetero molecules

B: GAMMA-CARDIOTOXIN
hetero molecules

B: GAMMA-CARDIOTOXIN
hetero molecules

C: GAMMA-CARDIOTOXIN
hetero molecules

C: GAMMA-CARDIOTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,02334
Polymers41,0316
Non-polymers99328
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area6740 Å2
ΔGint-265 kcal/mol
Surface area22510 Å2
MethodPISA
4
A: GAMMA-CARDIOTOXIN
hetero molecules

A: GAMMA-CARDIOTOXIN
hetero molecules

B: GAMMA-CARDIOTOXIN
hetero molecules

B: GAMMA-CARDIOTOXIN
hetero molecules

C: GAMMA-CARDIOTOXIN
hetero molecules

C: GAMMA-CARDIOTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,02334
Polymers41,0316
Non-polymers99328
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_444x-1/2,y-1/2,z-11
crystal symmetry operation4_647-x+3/2,y-1/2,-z+21
crystal symmetry operation3_546x+1/2,y-1/2,z+11
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area5560 Å2
ΔGint-248 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.670, 40.710, 56.020
Angle α, β, γ (deg.)90.00, 117.08, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 9 / 2: CIS PROLINE - PRO B 9 / 3: CIS PROLINE - PRO C 9
4: SOLVENT MOLECULE IN SPECIAL POSITION ON CRYSTAL TWO-FOLD AXIS.
Components on special symmetry positions
IDModelComponents
11A-120-

CL

21A-273-

HOH

31B-277-

HOH

41B-292-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.47938, -0.87748, -0.01495), (0.87616, -0.4795, 0.04924), (-0.05038, 0.01051, 0.99868)46.66, -11.16, 0.82
2given(-0.64021, 0.76745, 0.03388), (-0.7682, -0.63967, -0.02625), (0.00152, -0.04283, 0.99908)38.39, 37.31, 1.19
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein GAMMA-CARDIOTOXIN


Mass: 6838.462 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja nigricollis (spitting cobra) / References: UniProt: P01468
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details14 SOLVENT MOLECULES WERE IDENTIFIED AS CHLORIDE ANIONS, BASED ON THEIR HIGH OCCUPANCY, WHEN ...14 SOLVENT MOLECULES WERE IDENTIFIED AS CHLORIDE ANIONS, BASED ON THEIR HIGH OCCUPANCY, WHEN REFINED AS WATER, AND ON THEIR PROXIMITY TO POSITIVE CHARGES OF THE PROTEIN (THE MOTHER LIQUOR IS A SOLUTION OF NACL).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, sitting drop / Details: macro seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
22.2-2.4 M1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 2.3 Å / Num. obs: 17217 / % possible obs: 100 % / Num. measured all: 56659 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.6 Å / % possible obs: 40 %

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.55→5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.172 -
obs0.172 16149
Refinement stepCycle: LAST / Resolution: 1.55→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 14 164 1582
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.74.7
X-RAY DIFFRACTIONx_mcangle_it5.25.2
X-RAY DIFFRACTIONx_scbond_it9.79.7
X-RAY DIFFRACTIONx_scangle_it1111
Refinement
*PLUS
Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.050.044
X-RAY DIFFRACTIONx_planar_d0.070.057
X-RAY DIFFRACTIONx_plane_restr0.030.021
X-RAY DIFFRACTIONx_chiral_restr0.160.111

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