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- PDB-3q8e: Crystal structure of Protective Antigen W346F (pH 8.5) -

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Basic information

Entry
Database: PDB / ID: 3q8e
TitleCrystal structure of Protective Antigen W346F (pH 8.5)
ComponentsProtective antigen
KeywordsTOXIN / Protective Antigen / Anthrax / pH stability
Function / homology
Function and homology information


: / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding ...: / host cell cytosol / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane / metal ion binding
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 / Bacterial exotoxin B / Protective antigen, heptamerisation domain ...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 / 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 / FOURIER SYNTHESIS / Resolution: 2.098 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 1.3Sep 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_asym_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_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
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.372, 93.601, 117.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 25%(w/v) PEG 1500, 100mM SPG Buffer, pH 8.5, 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: 2.098→117.205 Å / Num. all: 46703 / Num. obs: 46703 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.06 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.216.30.491.54228167210.49100
2.21-2.356.30.342.24035063750.34100
2.35-2.516.60.2223.43956459790.222100
2.51-2.716.50.1514.93658655940.151100
2.71-2.976.30.1027.53241851650.102100
2.97-3.326.50.06311.73068546950.06399.9
3.32-3.836.30.04216.22612941690.04299.9
3.83-4.695.90.03220.12110735690.03299.9
4.69-6.636.30.02822.61762427960.02899.9
6.63-117.2055.70.02324.9937016400.02399.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3MHZ

3mhz


Resolution: 2.098→45.291 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.35 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 2352 5.06 %RANDOM
Rwork0.194 ---
obs0.1967 46482 99.6 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.297 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 118.48 Å2 / Biso mean: 44.9292 Å2 / Biso min: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--8.963 Å2-0 Å20 Å2
2---9.7716 Å2-0 Å2
3---18.7346 Å2
Refinement stepCycle: LAST / Resolution: 2.098→45.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 2 243 5615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125462
X-RAY DIFFRACTIONf_angle_d1.2827418
X-RAY DIFFRACTIONf_chiral_restr0.075855
X-RAY DIFFRACTIONf_plane_restr0.006969
X-RAY DIFFRACTIONf_dihedral_angle_d14.4642012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.098-2.1730.3392550.241443414596100
2.173-2.260.29732250.224943474572100
2.26-2.36280.33672290.24474301453098
2.3628-2.48740.29842330.20884337457099
2.4874-2.64320.32012180.210244034621100
2.6432-2.84730.29642170.221744214638100
2.8473-3.13380.30872400.219344094649100
3.1338-3.58710.24062150.20544684683100
3.5871-4.51870.21262430.15344734716100
4.5187-45.30180.19042770.174946304907100

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