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- PDB-4h2a: Crystal structure of wild type protective antigen to 1.62 A (pH 7.5) -

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Basic information

Entry
Database: PDB / ID: 4h2a
TitleCrystal structure of wild type protective antigen to 1.62 A (pH 7.5)
ComponentsProtective antigen
KeywordsTOXIN / toxin delivery / metal ion binding / protein binding / extracellular region
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 / Resolution: 1.62 Å
AuthorsBaker, P.J. / Sorrell, F.J.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of wild type protective antigen to 1.62 A (pH 7.5)
Authors: Sorrell, F.J. / Rodgers, H.F. / Baker, P.J. / Chen, B.
History
DepositionSep 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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)83,0977
Polymers82,7691
Non-polymers3286
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.050, 94.090, 117.390
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: 82768.828 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P13423
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein crystallised from 0.1 M HEPES pH 7.5, 10 % PEG 8000, 8 % ethylene glycol by sitting drop vapour diffusion at temperature 280 K., VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2010
RadiationMonochromator: Diamond I03 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.62→37.62 Å / Num. all: 103686 / Num. obs: 103686 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.62-1.663.60.722.17629199.9
7.25-37.623.10.02538.4899170.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACC

1acc


Resolution: 1.62→37.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.923 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 5155 5 %RANDOM
Rwork0.1874 ---
all0.189 103111 --
obs0.189 103111 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.83 Å2 / Biso mean: 30.0529 Å2 / Biso min: 8.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---1.62 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.62→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 18 556 6167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025742
X-RAY DIFFRACTIONr_bond_other_d0.0010.023881
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9567781
X-RAY DIFFRACTIONr_angle_other_deg0.87339535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80325.663279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.758151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.31528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
LS refinement shellResolution: 1.62→1.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 389 -
Rwork0.284 6768 -
all-7157 -
obs--99.06 %

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