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Basic information

Entry
Database: PDB / ID: 3hvd
TitleThe Protective Antigen Component of Anthrax Toxin Forms Functional Octameric Complexes
ComponentsProtective antigen
KeywordsTRANSPORT PROTEIN / TOXIN / Bacillus Anthracis / Anthrax Protective Antigen / Octamer / Xray-Crystallography
Function / homology
Function and homology information


: / protein homooligomerization / extracellular region / metal ion binding
Similarity search - Function
Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / 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 ...Protective antigen, heptamerisation domain / Immunoglobulin-like - #810 / Ubiquitin-like (UB roll) - #110 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å
AuthorsKintzer, A.F. / Dong, K.C. / Berger, J.M. / Krantz, B.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The protective antigen component of anthrax toxin forms functional octameric complexes.
Authors: Kintzer, A.F. / Thoren, K.L. / Sterling, H.J. / Dong, K.C. / Feld, G.K. / Tang, I.I. / Zhang, T.T. / Williams, E.R. / Berger, J.M. / Krantz, B.A.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protective antigen
B: Protective antigen
C: Protective antigen
D: Protective antigen
E: Protective antigen
F: Protective antigen
G: Protective antigen
H: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,74024
Polymers492,0998
Non-polymers64116
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
A: Protective antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5933
Polymers61,5121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.602, 125.670, 125.823
Angle α, β, γ (deg.)106.64, 110.82, 110.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 174:273 or resseq 287:302 or resseq...A174 - 273
121chain A and (resseq 174:273 or resseq 287:302 or resseq...A287 - 302
131chain A and (resseq 174:273 or resseq 287:302 or resseq...A327 - 338
141chain A and (resseq 174:273 or resseq 287:302 or resseq...A345 - 734
151chain A and (resseq 174:273 or resseq 287:302 or resseq...A736 - 739
211chain C and (resseq 174:273 or resseq 287:302 or resseq...C174 - 273
221chain C and (resseq 174:273 or resseq 287:302 or resseq...C287 - 302
231chain C and (resseq 174:273 or resseq 287:302 or resseq...C327 - 338
241chain C and (resseq 174:273 or resseq 287:302 or resseq...C345 - 734
251chain C and (resseq 174:273 or resseq 287:302 or resseq...C736 - 739
311chain E and (resseq 174:273 or resseq 287:302 or resseq...E174 - 273
321chain E and (resseq 174:273 or resseq 287:302 or resseq...E287 - 302
331chain E and (resseq 174:273 or resseq 287:302 or resseq...E327 - 338
341chain E and (resseq 174:273 or resseq 287:302 or resseq...E345 - 734
351chain E and (resseq 174:273 or resseq 287:302 or resseq...E736 - 739
411chain G and (resseq 174:273 or resseq 287:302 or resseq...G174 - 273
421chain G and (resseq 174:273 or resseq 287:302 or resseq...G287 - 302
431chain G and (resseq 174:273 or resseq 287:302 or resseq...G327 - 338
441chain G and (resseq 174:273 or resseq 287:302 or resseq...G345 - 734
451chain G and (resseq 174:273 or resseq 287:302 or resseq...G736 - 739
112chain B and (resseq 174:273 or resseq 287:302 or resseq...B174 - 273
122chain B and (resseq 174:273 or resseq 287:302 or resseq...B287 - 302
132chain B and (resseq 174:273 or resseq 287:302 or resseq...B327 - 338
142chain B and (resseq 174:273 or resseq 287:302 or resseq...B345 - 734
152chain B and (resseq 174:273 or resseq 287:302 or resseq...B736 - 739
212chain D and (resseq 174:273 or resseq 287:302 or resseq...D174 - 273
222chain D and (resseq 174:273 or resseq 287:302 or resseq...D287 - 302
232chain D and (resseq 174:273 or resseq 287:302 or resseq...D327 - 338
242chain D and (resseq 174:273 or resseq 287:302 or resseq...D345 - 734
252chain D and (resseq 174:273 or resseq 287:302 or resseq...D736 - 739
312chain F and (resseq 174:273 or resseq 287:302 or resseq...F174 - 273
322chain F and (resseq 174:273 or resseq 287:302 or resseq...F287 - 302
332chain F and (resseq 174:273 or resseq 287:302 or resseq...F327 - 338
342chain F and (resseq 174:273 or resseq 287:302 or resseq...F345 - 734
352chain F and (resseq 174:273 or resseq 287:302 or resseq...F736 - 739
412chain H and (resseq 174:273 or resseq 287:302 or resseq...H174 - 273
422chain H and (resseq 174:273 or resseq 287:302 or resseq...H287 - 302
432chain H and (resseq 174:273 or resseq 287:302 or resseq...H327 - 338
442chain H and (resseq 174:273 or resseq 287:302 or resseq...H345 - 734
452chain H and (resseq 174:273 or resseq 287:302 or resseq...H736 - 739

NCS ensembles :
ID
1
2

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Components

#1: Protein
Protective antigen


Mass: 61512.352 Da / Num. of mol.: 8 / Fragment: Membrane Insertion Loop (305-324) Deleted / Mutation: V303P,H304G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pa, PAG / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08G54
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CRYSTALLIZED PROTEIN IS A MEMBRANE INSERTION LOOP (MIL)-DELETED VARIANT OF WILD TYPE PA. ...THE CRYSTALLIZED PROTEIN IS A MEMBRANE INSERTION LOOP (MIL)-DELETED VARIANT OF WILD TYPE PA. RESIDUES 305-324 WERE DELETED, ENCOMPASSING THE MIL. IN THE PROCESS, TWO POINT MUTATIONS (V303P AND H304G) WERE INTRODUCED, ULTIMATELY TO REPLACE THE MIL WITH A TYPE II TURN. RESIDUE NUMBERING IS EXACTLY AS IN PDB 1ACC
Sequence detailsTHE RESIDUE AT POSITION 669 IS ARG, AS LISTED IN UNP ENTRY P13423. R669 IS LIKELY THE WILD TYPE ...THE RESIDUE AT POSITION 669 IS ARG, AS LISTED IN UNP ENTRY P13423. R669 IS LIKELY THE WILD TYPE SEQUENCE RESIDUE

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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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 74 mM sodium acetate, 7 mM Tris, 0.62 M NaCl, 37 mM tetrabutylammonium bromide, 7% ethanol, 0.07% n-dodecyl-D-maltopyranoside, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0712 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0712 Å / Relative weight: 1
ReflectionResolution: 3.209→47.2745 Å / Num. all: 94967 / Num. obs: 87387 / % possible obs: 98.14 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 10.78
Reflection shellResolution: 3.209→3.2451 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.1 / Num. unique all: 94967 / Rsym value: 0.595 / % possible all: 90.28

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TZO

1tzo


Resolution: 3.209→47.274 Å / SU ML: 3.22 / σ(F): 0.14 / σ(I): 2.07 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 4392 5.03 %RANDOM
Rwork0.2099 ---
all0.2118 94967 --
obs0.2118 87347 90.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.402 Å2 / ksol: 0.264 e/Å3
Refinement stepCycle: LAST / Resolution: 3.209→47.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32677 0 16 8 32701
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4050X-RAY DIFFRACTIONPOSITIONAL0.01
12C4050X-RAY DIFFRACTIONPOSITIONAL0.01
13E4051X-RAY DIFFRACTIONPOSITIONAL0.007
14G4054X-RAY DIFFRACTIONPOSITIONAL0.017
21B4036X-RAY DIFFRACTIONPOSITIONAL0.013
22D4036X-RAY DIFFRACTIONPOSITIONAL0.013
23F4046X-RAY DIFFRACTIONPOSITIONAL0.015
24H4042X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.209-3.24510.37991090.30952098X-RAY DIFFRACTION68
3.2451-3.28320.35961390.29682536X-RAY DIFFRACTION83
3.2832-3.32330.35961300.29322581X-RAY DIFFRACTION84
3.3233-3.36530.35011140.2852513X-RAY DIFFRACTION84
3.3653-3.40960.30111430.26722616X-RAY DIFFRACTION84
3.4096-3.45630.33931360.26442620X-RAY DIFFRACTION86
3.4563-3.50560.31741510.24972716X-RAY DIFFRACTION87
3.5056-3.5580.28911340.24432664X-RAY DIFFRACTION88
3.558-3.61350.30961240.23152770X-RAY DIFFRACTION89
3.6135-3.67280.24311380.22742805X-RAY DIFFRACTION91
3.6728-3.73610.28071380.21262785X-RAY DIFFRACTION92
3.7361-3.8040.24981500.19332817X-RAY DIFFRACTION91
3.804-3.87710.25731530.20132642X-RAY DIFFRACTION88
3.8771-3.95620.22511720.18692769X-RAY DIFFRACTION90
3.9562-4.04220.23231430.19812683X-RAY DIFFRACTION87
4.0422-4.13620.20041350.18622679X-RAY DIFFRACTION89
4.1362-4.23950.26451520.17972762X-RAY DIFFRACTION90
4.2395-4.35410.23981580.1812814X-RAY DIFFRACTION92
4.3541-4.48210.20551570.17042883X-RAY DIFFRACTION92
4.4821-4.62670.20161310.14972816X-RAY DIFFRACTION93
4.6267-4.79190.16861420.14422794X-RAY DIFFRACTION92
4.7919-4.98350.16631680.13782876X-RAY DIFFRACTION94
4.9835-5.21010.20381350.15852921X-RAY DIFFRACTION94
5.2101-5.48440.20831620.16452961X-RAY DIFFRACTION96
5.4844-5.82740.22271500.16672872X-RAY DIFFRACTION96
5.8274-6.27640.23261580.16933011X-RAY DIFFRACTION96
6.2764-6.90630.20121530.17522943X-RAY DIFFRACTION97
6.9063-7.90160.19481750.16092990X-RAY DIFFRACTION98
7.9016-9.940.14231730.14562990X-RAY DIFFRACTION99
9.94-47.27960.18881690.20743028X-RAY DIFFRACTION99

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