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- PDB-1tzo: Crystal Structure of the Anthrax Toxin Protective Antigen Heptame... -

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Basic information

Entry
Database: PDB / ID: 1tzo
TitleCrystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore
ComponentsProtective antigen
KeywordsTOXIN / heptamer
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding ...positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane / metal ion binding
Similarity search - Function
Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 ...Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Ubiquitin-like (UB roll) / Jelly Rolls / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLacy, D.B. / Wigelsworth, D.J. / Melnyk, R.A. / Collier, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structure of heptameric protective antigen bound to an anthrax toxin receptor: A role for receptor in pH-dependent pore formation
Authors: Lacy, D.B. / Wigelsworth, D.J. / Melnyk, R.A. / Harrison, S.C. / Collier, R.J.
History
DepositionJul 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protective antigen
B: Protective antigen
C: Protective antigen
D: Protective antigen
E: Protective antigen
F: Protective antigen
G: Protective antigen
H: Protective antigen
I: Protective antigen
J: Protective antigen
K: Protective antigen
L: Protective antigen
M: Protective antigen
O: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)883,38842
Polymers882,26614
Non-polymers1,12228
Water00
1
A: Protective antigen
B: Protective antigen
C: Protective antigen
D: Protective antigen
E: Protective antigen
F: Protective antigen
O: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,69421
Polymers441,1337
Non-polymers56114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28240 Å2
ΔGint-85 kcal/mol
Surface area169440 Å2
MethodPISA
2
G: Protective antigen
H: Protective antigen
I: Protective antigen
J: Protective antigen
K: Protective antigen
L: Protective antigen
M: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,69421
Polymers441,1337
Non-polymers56114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28240 Å2
ΔGint-83 kcal/mol
Surface area169450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.608, 167.028, 168.200
Angle α, β, γ (deg.)77.56, 75.74, 76.01
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
DetailsThe biological assembly is one heptamer

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Components

#1: Protein
Protective antigen / pXO1-110 / PA-83 / PA83


Mass: 63019.012 Da / Num. of mol.: 14 / Fragment: 63-kDa domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: A2012 / Gene: pagA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3 Star / References: UniProt: P13423
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ca

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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: 4.4 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: HEPES, sodium chloride, b-octylglucoside, spermine, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 2000 / Details: mirrors
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.6→30 Å / Num. all: 163256 / Num. obs: 163256 / % possible obs: 93.4 % / Observed criterion σ(I): 1.6 / Redundancy: 2 % / Rsym value: 0.048 / Net I/σ(I): 10.6
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 12081 / Rsym value: 0.291 / % possible all: 68.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4.5 PA heptamer model

Resolution: 3.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.317 7979 -random
Rwork0.314 ---
all0.315 163256 --
obs0.315 162885 93.2 %-
Refinement stepCycle: LAST / Resolution: 3.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61110 0 28 0 61138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_angle_deg1.097

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