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- PDB-5fr3: X-ray crystal structure of aggregation-resistant protective antig... -

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Basic information

Entry
Database: PDB / ID: 5fr3
TitleX-ray crystal structure of aggregation-resistant protective antigen of Bacillus anthracis (mutant S559L T576E)
ComponentsPROTECTIVE ANTIGEN
KeywordsTOXIN / ANTHRAX PROTECTIVE ANTIGEN
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 / identical protein binding ...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 / 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 / Resolution: 1.935 Å
AuthorsGanesan, A. / Siekierska, A. / Beerten, J. / Brams, M. / van Durme, J. / De Baets, G. / van der Kant, R. / Gallardo, R. / Ramakers, M. / Langenberg, T. ...Ganesan, A. / Siekierska, A. / Beerten, J. / Brams, M. / van Durme, J. / De Baets, G. / van der Kant, R. / Gallardo, R. / Ramakers, M. / Langenberg, T. / Wilkinson, H. / De Smet, F. / Ulens, C. / Rousseau, F. / Schymkowitz, J.
CitationJournal: Nat.Commun. / Year: 2016
Title: Structural Hot Spots for the Solubility of Globular Proteins
Authors: Ganesan, A. / Siekierska, A. / Beerten, J. / Brams, M. / Van Durme, J. / De Baets, G. / Van Der Kant, R. / Gallardo, R. / Ramakers, M. / Langenberg, T. / Wilkinson, H. / De Smet, F. / Ulens, ...Authors: Ganesan, A. / Siekierska, A. / Beerten, J. / Brams, M. / Van Durme, J. / De Baets, G. / Van Der Kant, R. / Gallardo, R. / Ramakers, M. / Langenberg, T. / Wilkinson, H. / De Smet, F. / Ulens, C. / Rousseau, F. / Schymkowitz, J.
History
DepositionDec 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references / Structure summary
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: PROTECTIVE ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5165
Polymers81,2511
Non-polymers2644
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.547, 94.714, 100.627
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 / ANTHRAX PROTECTIVE ANTIGEN


Mass: 81251.227 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Description: SYNTHETIC GENE / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.6 Å3/Da / Density % sol: 52.78 % / Description: NONE
Crystal growDetails: 20 MM MGCL2, 100 MM HEPES PH 7.5, 22% POLY(ACRYLIC ACID SODIUM SALT) 5100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92045
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92045 Å / Relative weight: 1
ReflectionResolution: 1.94→44.45 Å / Num. obs: 203741 / % possible obs: 98.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 25.48 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 8
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.4 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACC

1acc


Resolution: 1.935→44.433 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 2016 3.3 %
Rwork0.1781 --
obs0.1798 60664 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.935→44.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5444 0 14 667 6125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055602
X-RAY DIFFRACTIONf_angle_d0.9537599
X-RAY DIFFRACTIONf_dihedral_angle_d14.0252103
X-RAY DIFFRACTIONf_chiral_restr0.068862
X-RAY DIFFRACTIONf_plane_restr0.004992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.935-1.98340.30591460.273905X-RAY DIFFRACTION95
1.9834-2.03710.31881440.24014139X-RAY DIFFRACTION100
2.0371-2.0970.26161270.21994192X-RAY DIFFRACTION100
2.097-2.16470.29291530.2124157X-RAY DIFFRACTION100
2.1647-2.24210.23611360.19854135X-RAY DIFFRACTION100
2.2421-2.33180.23881340.19074185X-RAY DIFFRACTION100
2.3318-2.43790.24241580.18884162X-RAY DIFFRACTION100
2.4379-2.56650.26251340.18494200X-RAY DIFFRACTION100
2.5665-2.72720.24161520.18754196X-RAY DIFFRACTION100
2.7272-2.93780.2541460.17914196X-RAY DIFFRACTION100
2.9378-3.23330.21731460.17654207X-RAY DIFFRACTION100
3.2333-3.7010.21691430.15764239X-RAY DIFFRACTION100
3.701-4.66210.17121450.1434290X-RAY DIFFRACTION100
4.6621-44.4450.21211520.17294445X-RAY DIFFRACTION100
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)
12.93291.32150.54453.08290.5184.51570.01540.4872-0.3944-0.09870.17360.01570.49070.0087-0.14010.31840.0933-0.04220.414-0.07190.2244-4.2084-42.166-23.8495
20.6680.0167-0.4460.6276-0.17793.66180.05160.01660.00290.0014-0.0212-0.00340.26830.0383-0.02410.1730.080.00120.13490.00580.1883-1.5792-29.226916.006
31.2634-0.4335-1.05950.94291.15122.4691-0.0407-0.03030.2447-0.0173-0.12950.1338-0.0451-0.0990.10840.16780.0441-0.02810.1428-0.04550.2948-8.1462-5.084827.2328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 14:177)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 178:521)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 522:735)

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