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- PDB-3tex: Crystal Structure of Anthrax Protective Antigen (Membrane Inserti... -

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Basic information

Entry
Database: PDB / ID: 3tex
TitleCrystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) to 1.7-A resolution
ComponentsProtective antigen
Keywordsprotein transport / toxin
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 / membrane ...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 / membrane / identical protein binding / metal ion binding
Similarity search - Function
Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / 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 ...Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFeld, G.K. / Krantz, B.A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Domain flexibility modulates the heterogeneous assembly mechanism of anthrax toxin protective antigen.
Authors: Feld, G.K. / Kintzer, A.F. / Tang, I.I. / Thoren, K.L. / Krantz, B.A.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Feb 28, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8143
Polymers80,7341
Non-polymers802
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.396, 93.937, 117.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protective antigen / PA / Anthrax toxins translocating protein / PA-83 / PA83 / Protective antigen PA-20 / PA20 / ...PA / Anthrax toxins translocating protein / PA-83 / PA83 / Protective antigen PA-20 / PA20 / Protective antigen PA-63 / PA63


Mass: 80733.641 Da / Num. of mol.: 1 / Mutation: V303P,H304G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BXA0164, GBAA_pXO1_0164, pag, pagA, PX01, pXO1-110 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21) / References: UniProt: P13423*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CLOSEST DATABASE REFERENCE TO THE CRYSTALLIZED SEQUENCE CORRESPONDS TO UNP ENTRY P13423, WHICH ...THE CLOSEST DATABASE REFERENCE TO THE CRYSTALLIZED SEQUENCE CORRESPONDS TO UNP ENTRY P13423, WHICH CONTAINS A PRESEQUENCE THAT IS NOT INCLUDED IN NATURAL ANTHRAX PA, NOR WAS A PART OF THE PROTEIN CRYSTALLIZED. THE RESIDUE NUMBERS IN THIS STRUCTURE CONFORM TO THE SEQUENCE FOR PDB ACCESSION CODE 1ACC. TO CLARIFY IN TERMS OF UNP SEQUENCE, THE MUTATIONS MADE WERE V332P AND H333G.

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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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% (15/4 EO/OH), 0.05M bis-tris-Cl, 0.05M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2011
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.7→9.99 Å / Num. all: 87171 / Num. obs: 87171 / % possible obs: 99.8 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 8.1 % / Biso Wilson estimate: 27.278 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 22.1
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5315 / Rsym value: 0.855 / % possible all: 80

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→9.986 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 1879 2.29 %Random
Rwork0.1938 ---
all0.1943 87171 --
obs0.1943 82026 93.95 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.001 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.6576 Å2-0 Å20 Å2
2---7.4943 Å2-0 Å2
3---15.3445 Å2
Refinement stepCycle: LAST / Resolution: 1.7→9.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 2 399 5969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075692
X-RAY DIFFRACTIONf_angle_d1.0537723
X-RAY DIFFRACTIONf_dihedral_angle_d13.5312161
X-RAY DIFFRACTIONf_chiral_restr0.073874
X-RAY DIFFRACTIONf_plane_restr0.0041012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6995-1.74520.34941160.28045199X-RAY DIFFRACTION80
1.7452-1.79620.29731290.24735471X-RAY DIFFRACTION85
1.7962-1.85390.261250.22455654X-RAY DIFFRACTION87
1.8539-1.91970.26441420.21465836X-RAY DIFFRACTION90
1.9197-1.9960.2491420.21286050X-RAY DIFFRACTION93
1.996-2.0860.26341480.21086270X-RAY DIFFRACTION96
2.086-2.19490.23761530.20946353X-RAY DIFFRACTION97
2.1949-2.33080.20961500.19966355X-RAY DIFFRACTION97
2.3308-2.50810.2471500.19646480X-RAY DIFFRACTION98
2.5081-2.75570.23481530.2136480X-RAY DIFFRACTION99
2.7557-3.14350.21721550.21426537X-RAY DIFFRACTION99
3.1435-3.92020.19861560.18036650X-RAY DIFFRACTION100
3.9202-9.98630.18581600.16916812X-RAY DIFFRACTION100

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