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- PDB-3q8f: Crystal structure of 2-Fluorohistine labeled Protective Antigen (... -

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Basic information

Entry
Database: PDB / ID: 3q8f
TitleCrystal structure of 2-Fluorohistine labeled Protective Antigen (pH 5.8)
ComponentsProtective antigen
KeywordsPROTEIN BINDING / Protective Antigen / 2-Fluorohistidine / Anthrax / pH stability
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 / Direct Replacement / Resolution: 2.1 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_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.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.conn_type_id / _struct_conn.id / _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_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)83,4175
Polymers82,9491
Non-polymers4694
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.292, 93.657, 115.565
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: 82948.742 Da / Num. of mol.: 1
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) / Strain (production host): UTH780 / 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 30% PEG 400, 100mM MES, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.38 Å / Num. all: 46290 / Num. obs: 46290 / % possible obs: 98.41 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.43 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.2927
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.1-2.217.520.752.9649947664198.1
2.21-2.357.480.564.2747195631198.29
2.35-2.517.520.336.2644791595898.59
2.51-2.717.50.219.4141871558398.75
2.71-2.977.50.1114.2538588514598.88
2.97-3.327.460.0623.5335054469799.12
3.32-3.837.430.0441.1930814415099.2
3.83-4.77.350.0354.8626228356799.34
4.7-6.647.230.0259.9420317280999.53
6.64-45.386.450.0258.849213142987.95

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.16data scaling
PHENIXdev_601refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: Direct Replacement
Starting model: PDB entry 3MHZ

3mhz


Resolution: 2.1→43.401 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 0 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 2341 5.07 %RANDOM
Rwork0.222 ---
obs0.2243 46210 98.05 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.365 Å2 / ksol: 0.413 e/Å3
Displacement parametersBiso max: 99.61 Å2 / Biso mean: 52.9572 Å2 / Biso min: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1--4.9936 Å2-0 Å20 Å2
2---10.1634 Å2-0 Å2
3---15.157 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 28 124 5204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115172
X-RAY DIFFRACTIONf_angle_d1.2777032
X-RAY DIFFRACTIONf_chiral_restr0.072809
X-RAY DIFFRACTIONf_plane_restr0.006902
X-RAY DIFFRACTIONf_dihedral_angle_d15.6261893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14290.33821420.2862525266798
2.1429-2.18950.30711350.28552539267498
2.1895-2.24040.3591280.27462552268098
2.2404-2.29640.33851220.2812564268698
2.2964-2.35850.25521700.25592515268598
2.3585-2.42790.30931300.24372566269698
2.4279-2.50630.31361290.25142545267498
2.5063-2.59580.2991500.24242571272198
2.5958-2.69970.30741490.25252565271499
2.6997-2.82260.34861330.24112603273699
2.8226-2.97140.34171290.24352580270999
2.9714-3.15750.2981320.23392598273099
3.1575-3.40120.26111340.22512627276199
3.4012-3.74330.24471310.21442619275099
3.7433-4.28450.23081280.19152658278699
4.2845-5.39640.20531500.1782658280899
5.3964-43.410.27341490.22872584273392

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