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- PDB-3q8c: Crystal structure of Protective Antigen W346F (pH 5.5) -

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Basic information

Entry
Database: PDB / ID: 3q8c
TitleCrystal structure of Protective Antigen W346F (pH 5.5)
ComponentsProtective antigen
KeywordsTOXIN / Protective Antigen / Anthrax / pH stability
Function / homology
Function and homology information


symbiont-mediated suppression of host MAPK cascade / host cell cytosol / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / metal ion binding / identical protein binding / membrane
Similarity search - Function
Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen, heptamerisation domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / PA14/GLEYA domain / PA14 domain profile. ...Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / Protective antigen, heptamerisation domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / PA14/GLEYA domain / PA14 domain profile. / 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 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 / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsLovell, S. / Battaile, K.P. / Rajapaksha, M. / Janowiak, B.E. / Andra, K.K. / Bann, J.G.
CitationJournal: Protein Sci. / Year: 2012
Title: pH effects on binding between the anthrax protective antigen and the host cellular receptor CMG2.
Authors: Rajapaksha, M. / Lovell, S. / Janowiak, B.E. / Andra, K.K. / Battaile, K.P. / Bann, J.G.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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)82,8103
Polymers82,7301
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.674, 94.053, 117.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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: 82729.789 Da / Num. of mol.: 1 / Mutation: W346F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pagA, pag, pXO1-110, BXA0164, GBAA_pXO1_0164 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / References: UniProt: P13423
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25%(w/v) PEG 1500, 100mM SPG Buffer, pH 5.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→35 Å / Num. all: 19416 / Num. obs: 19416 / % possible obs: 99.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.61 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4916
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.85-36.670.752.69186392793100
3-3.196.980.454.3618260261699.96
3.19-3.416.960.247.89174332504100
3.41-3.686.760.1412.48157042322100
3.68-4.036.280.116.7213462214499.98
4.03-4.516.340.0624.37123291946100
4.51-5.26.720.0530.1711732174599.97
5.2-6.376.560.0529.5196371468100
6.37-9.015.950.0433.5470601187100
9.01-355.950.0348.45411069198.28

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.16data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3MHZ

3mhz


Resolution: 2.85→34.708 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.45 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 991 5.12 %RANDOM
Rwork0.2092 ---
obs0.2124 19358 99.92 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.367 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 158.59 Å2 / Biso mean: 68.1292 Å2 / Biso min: 32.25 Å2
Baniso -1Baniso -2Baniso -3
1-14.2909 Å2-0 Å20 Å2
2---14.4796 Å2-0 Å2
3---0.1887 Å2
Refinement stepCycle: LAST / Resolution: 2.85→34.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 2 0 5244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075332
X-RAY DIFFRACTIONf_angle_d1.0367250
X-RAY DIFFRACTIONf_chiral_restr0.056841
X-RAY DIFFRACTIONf_plane_restr0.004947
X-RAY DIFFRACTIONf_dihedral_angle_d14.8271947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.85-3.00020.43941540.323525652719
3.0002-3.18810.31771260.265325762702
3.1881-3.4340.30761280.230426082736
3.434-3.77920.30261510.215625932744
3.7792-4.32520.24161340.180426182752
4.3252-5.44590.25921340.171126522786
5.4459-34.71060.23081640.210927552919

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