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- PDB-3ino: 1.95A Resolution Structure of Protective Antigen Domain 4 -

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Basic information

Entry
Database: PDB / ID: 3ino
Title1.95A Resolution Structure of Protective Antigen Domain 4
ComponentsProtective antigen PA-63
KeywordsIMMUNE SYSTEM / anthrax / domain 4 / protective antigen / toxin / Calcium / Cleavage on pair of basic residues / Metal-binding / Plasmid / Secreted / Virulence
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
Immunoglobulin-like - #810 / 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 ...Immunoglobulin-like - #810 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLovell, S. / Williams, A.S. / Anbanandam, A. / El-Chami, R. / Bann, J.G.
CitationJournal: Protein Sci. / Year: 2009
Title: Domain 4 of the anthrax protective antigen maintains structure and binding to the host receptor CMG2 at low pH
Authors: Williams, A.S. / Lovell, S. / Anbanandam, A. / El-Chami, R. / Bann, J.G.
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protective antigen PA-63
B: Protective antigen PA-63


Theoretical massNumber of molelcules
Total (without water)32,4852
Polymers32,4852
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protective antigen PA-63


Theoretical massNumber of molelcules
Total (without water)16,2421
Polymers16,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protective antigen PA-63


Theoretical massNumber of molelcules
Total (without water)16,2421
Polymers16,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.735, 35.851, 129.090
Angle α, β, γ (deg.)90.000, 99.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protective antigen PA-63 / PA63


Mass: 16242.256 Da / Num. of mol.: 2 / Fragment: Domain 4
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: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P13423
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG 8000, 100mM imidazole, 3% MPD, pH 6.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2009 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionAv R equivalents: 0.068 / Number: 65480
ReflectionResolution: 1.95→20 Å / Num. obs: 20573 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 25.127
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.302 / Rsym value: 0.291 / % possible all: 87.1
Cell measurementReflection used: 65480

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å18.95 Å
Translation2.2 Å18.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ACC

1acc


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.516 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1050 5.1 %RANDOM
Rwork0.199 ---
obs0.202 20573 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 58.67 Å2 / Biso mean: 29.871 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.21 Å2
2---0.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 0 111 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222286
X-RAY DIFFRACTIONr_bond_other_d00.022088
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9693089
X-RAY DIFFRACTIONr_angle_other_deg0.82734898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11625.185108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26915444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0631512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022526
X-RAY DIFFRACTIONr_gen_planes_other00.02438
X-RAY DIFFRACTIONr_mcbond_it0.9881.51395
X-RAY DIFFRACTIONr_mcbond_other0.2961.5581
X-RAY DIFFRACTIONr_mcangle_it1.71922273
X-RAY DIFFRACTIONr_scbond_it2.8063891
X-RAY DIFFRACTIONr_scangle_it4.5574.5807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.291680.2291250155484.813
2-2.0540.28720.2111330144497.091
2.054-2.1130.281790.2131376149697.259
2.113-2.1780.303680.2171261135598.081
2.178-2.2480.278740.2121302140697.866
2.248-2.3260.295480.2091214128698.134
2.326-2.4130.299740.1861233132998.345
2.413-2.5090.297570.2091128119599.163
2.509-2.6190.32600.2371116119598.41
2.619-2.7450.329520.2271078113699.472
2.745-2.890.256430.2141015106499.436
2.89-3.0610.288520.205987104199.808
3.061-3.2670.271480.198949997100
3.267-3.5210.258480.185838886100
3.521-3.8460.188480.174773821100
3.846-4.280.246340.169720754100
4.28-4.9050.173550.152643698100
4.905-5.9180.253310.199577608100
5.918-8.0260.28250.232432457100
8.026-200.202140.21630132098.438

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