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- PDB-4nam: 1.7A structure of 5-Fluoro Tryptophan Labeled Protective Antigen ... -

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Basic information

Entry
Database: PDB / ID: 4nam
Title1.7A structure of 5-Fluoro Tryptophan Labeled Protective Antigen (W206Y)
ComponentsProtective antigen
KeywordsTOXIN / anthrax / 5-fluorotryptophan / pore
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / 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 ...positive regulation of apoptotic process in another organism / 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 / 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 / molecular replacement / Resolution: 1.7 Å
AuthorsLovell, S. / Battaile, K.P. / Chadegani, F. / Mulangi, V. / Miyagi, M. / Bann, J.G.
CitationJournal: Biochemistry / Year: 2014
Title: (19)F nuclear magnetic resonance and crystallographic studies of 5-fluorotryptophan-labeled anthrax protective antigen and effects of the receptor on stability.
Authors: Chadegani, F. / Lovell, S. / Mullangi, V. / Miyagi, M. / Battaile, K.P. / Bann, J.G.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9343
Polymers82,8541
Non-polymers802
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.298, 93.954, 117.727
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: 82853.734 Da / Num. of mol.: 1 / Mutation: W206Y
Source method: isolated from a genetically manipulated source
Details: Tryptophan residues are labeled with 5-fluorotryptophan
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pagA, pag, pXO1-110, BXA0164, GBAA_pXO1_0164 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / 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.: 400 / 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: 48.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 35% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 0.05 M HEPES, 0.2 M Potassium chloride, pH 7.5, 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: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→73.435 Å / Num. all: 86339 / Num. obs: 86339 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 18.22 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4338 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.36 Å28.78 Å
Translation7.36 Å28.78 Å

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Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
PHASERphasing
PHENIXdev_1356refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHZ

3mhz


Resolution: 1.7→46.977 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.52 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 4149 5.01 %RANDOM
Rwork0.1794 ---
obs0.1809 82781 94.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.13 Å2 / Biso mean: 27.3545 Å2 / Biso min: 8.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 2 400 5692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095458
X-RAY DIFFRACTIONf_angle_d1.1087452
X-RAY DIFFRACTIONf_chiral_restr0.078869
X-RAY DIFFRACTIONf_plane_restr0.006971
X-RAY DIFFRACTIONf_dihedral_angle_d13.1352013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.26621510.24012516266794
1.7193-1.73960.24751460.23132602274895
1.7396-1.76080.28951470.22592553270094
1.7608-1.78310.2681310.22182620275194
1.7831-1.80650.23981390.21022553269294
1.8065-1.83130.27241290.21022563269293
1.8313-1.85740.19621430.19932535267894
1.8574-1.88520.21481360.20232544268092
1.8852-1.91460.25111120.2072502261490
1.9146-1.9460.26991280.21762318244686
1.946-1.97960.25531210.21832461258288
1.9796-2.01560.2141580.1852584274295
2.0156-2.05430.22641320.1752615274794
2.0543-2.09630.22271200.1832547266792
2.0963-2.14180.22631420.17472689283198
2.1418-2.19170.19521240.17372745286999
2.1917-2.24650.20641410.16462749289099
2.2465-2.30720.21541390.164627692908100
2.3072-2.37510.19091450.16492729287499
2.3751-2.45180.22031420.1732679282197
2.4518-2.53940.22951360.19142667280396
2.5394-2.6410.20211630.18952535269892
2.641-2.76120.25531180.20092439255788
2.7612-2.90680.24691530.1862667282096
2.9068-3.08890.20221270.18782717284497
3.0889-3.32730.21681410.17852764290599
3.3273-3.6620.15171460.17122770291698
3.662-4.19170.18751400.15052769290997
4.1917-5.27990.15231470.14182523267089
5.2799-46.99490.22661520.18772908306097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99430.21650.75050.5595-0.19461.7444-0.1289-0.07130.10270.0355-0.01840.1245-0.3474-0.2659-0.1780.23810.068-0.0860.1518-0.00560.1084-42.1857-8.78993.1145
21.212-0.21680.36140.18570.00130.3072-0.0459-0.01350.1283-0.03340.0078-0.0612-0.03370.024-0.00440.1015-0.0063-0.00850.10150.00780.114-4.4954-18.279723.4271
30.79020.19580.16340.25770.13780.1196-0.0461-0.0663-0.03970.01150.0521-0.0302-0.01660.00270.00240.10130.0065-0.00040.10170.02080.0886-10.3627-26.560426.8387
40.9649-0.0848-0.37921.57850.57570.60750.04870.0672-0.0879-0.2599-0.0571-0.0154-0.0625-0.0222-0.00010.15990.0337-0.02160.13330.00310.177720.478-44.77322.041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 175 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 408 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 603 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 604 through 734 )A0

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