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- PDB-3tez: Crystal Structure of Anthrax Protective Antigen Mutant S337C N664... -

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Basic information

Entry
Database: PDB / ID: 3tez
TitleCrystal Structure of Anthrax Protective Antigen Mutant S337C N664C and dithiolacetone modified to 1.8-A resolution
ComponentsProtective antigen
KeywordsPROTEIN TRANSPORT / TOXIN / Translocase
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
ACETONE / 2-METHOXYETHANOL / Protective antigen
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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

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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)83,0646
Polymers82,7741
Non-polymers2905
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.293, 93.686, 117.851
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: 82773.930 Da / Num. of mol.: 1 / Mutation: S337C,N664C
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 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21) / References: UniProt: P13423
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MXE / 2-METHOXYETHANOL / 2-Methoxyethanol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-ACN / ACETONE / Acetone


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG-ME 2000, 0.1M Tris-Cl, 0.2M Trimethylamine-N-oxide, pH 8.5, 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 5, 2011
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.83→24.9 Å / Num. all: 70160 / Num. obs: 70160 / % possible obs: 99.7 % / Observed criterion σ(F): 4.3 / Observed criterion σ(I): 4.3 / Redundancy: 14.2 % / Biso Wilson estimate: 26.49 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 20.9
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 4.3 / Num. unique all: 4105 / Rsym value: 0.757 / % possible all: 83

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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: 1.83→24.9 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1910 2.84 %Random
Rwork0.1926 ---
all0.1935 70160 --
obs0.1935 67310 95.61 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.4126 Å2-0 Å20 Å2
2---4.9184 Å2-0 Å2
3---16.6992 Å2
Refinement stepCycle: LAST / Resolution: 1.83→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 16 422 5998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165704
X-RAY DIFFRACTIONf_angle_d1.0877725
X-RAY DIFFRACTIONf_dihedral_angle_d12.7862159
X-RAY DIFFRACTIONf_chiral_restr0.071873
X-RAY DIFFRACTIONf_plane_restr0.0041012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8285-1.87420.25531130.25293992X-RAY DIFFRACTION83
1.8742-1.92490.29091250.2094271X-RAY DIFFRACTION89
1.9249-1.98150.26231340.20084414X-RAY DIFFRACTION91
1.9815-2.04540.23131330.20424520X-RAY DIFFRACTION94
2.0454-2.11850.2591330.20774646X-RAY DIFFRACTION96
2.1185-2.20320.25991370.20394671X-RAY DIFFRACTION97
2.2032-2.30340.25811370.20034714X-RAY DIFFRACTION96
2.3034-2.42480.26091370.2014728X-RAY DIFFRACTION98
2.4248-2.57660.25891410.21014762X-RAY DIFFRACTION98
2.5766-2.77530.27231400.21584817X-RAY DIFFRACTION99
2.7753-3.05410.24671410.20464845X-RAY DIFFRACTION99
3.0541-3.4950.19521430.18924911X-RAY DIFFRACTION100
3.495-4.39940.17751460.16674969X-RAY DIFFRACTION100
4.3994-24.94210.21771500.18255140X-RAY DIFFRACTION100

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