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- PDB-3etb: Crystal structure of the engineered neutralizing antibody M18 com... -

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Basic information

Entry
Database: PDB / ID: 3etb
TitleCrystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4
Components
  • Anthrax Protective Antigen
  • Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
KeywordsIMMUNE SYSTEM/TOXIN / single-chain FV / monoclonal antibody / immunoglobulin / toxin / antibody-antigen complex / IMMUNE SYSTEM-TOXIN COMPLEX
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 / membrane ...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 / membrane / identical protein binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Bacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsMonzingo, A.F. / Leysath, C.E. / Barnett, J. / Iverson, B.L. / Georgiou, G. / Robertus, J.D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen.
Authors: Leysath, C.E. / Monzingo, A.F. / Maynard, J.A. / Barnett, J. / Georgiou, G. / Iverson, B.L. / Robertus, J.D.
History
DepositionOct 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
G: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
H: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
I: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
J: Anthrax Protective Antigen
K: Anthrax Protective Antigen
L: Anthrax Protective Antigen
M: Anthrax Protective Antigen


Theoretical massNumber of molelcules
Total (without water)173,4658
Polymers173,4658
Non-polymers00
Water0
1
F: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
J: Anthrax Protective Antigen


Theoretical massNumber of molelcules
Total (without water)43,3662
Polymers43,3662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
K: Anthrax Protective Antigen


Theoretical massNumber of molelcules
Total (without water)43,3662
Polymers43,3662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
L: Anthrax Protective Antigen


Theoretical massNumber of molelcules
Total (without water)43,3662
Polymers43,3662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
M: Anthrax Protective Antigen


Theoretical massNumber of molelcules
Total (without water)43,3662
Polymers43,3662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.940, 299.720, 68.950
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains 4 biological units.

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Components

#1: Antibody
Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker


Mass: 26866.584 Da / Num. of mol.: 4
Mutation: I21V, L46F, S56P, S76N, Q78L, L94P, S1030N, T1058S, K1065E, T1069I
Source method: isolated from a genetically manipulated source
Details: periplasm / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): Jude-1
#2: Protein
Anthrax Protective Antigen / PA / PA-83 / PA83 / Anthrax toxins translocating protein [Contains: Protective antigen PA-20 and ...PA / PA-83 / PA83 / Anthrax toxins translocating protein [Contains: Protective antigen PA-20 and Protective antigen PA-63]


Mass: 16499.588 Da / Num. of mol.: 4
Fragment: Domain 4 of protective antigen PA-63: UNP residues 621-764
Source method: isolated from a genetically manipulated source
Details: secreted / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pagA, pag, pXO1-110, BXA0164, GBAA_pXO1_0164 / Plasmid: PX01 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): avirulent / References: UniProt: P13423
Sequence detailsRESIDUE NUMBERS FOR ANTIBODY M18 HEAVY CHAIN FRAGMENT HAVE OFFSET 1000 TO DISTINGUISH THEM FROM THE ...RESIDUE NUMBERS FOR ANTIBODY M18 HEAVY CHAIN FRAGMENT HAVE OFFSET 1000 TO DISTINGUISH THEM FROM THE ANTIBODY M18 LIGHT CHAIN FRAGMENT WHICH HAS ORIGINAL RESIDUE NUMBERING.

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 27, 2006 / Details: blue max-flux confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 18357 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.12 / Χ2: 1.042 / Net I/σ(I): 6.1
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.283 / Num. unique all: 1705 / Χ2: 1.35 / % possible all: 91.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3ESU, 1ACC

3esu

1acc


Resolution: 3.8→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.837 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Non-crystallographic symmetry restraints have been used for positional refinement. Group B factors were refined (2 per residue).
RfactorNum. reflection% reflectionSelection details
Rfree0.276 819 4.3 %random
Rwork0.232 ---
all0.232 16142 --
obs0.232 16142 83.8 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso max: 100 Å2 / Biso mean: 13.505 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1--5.039 Å20 Å25.704 Å2
2---4.314 Å20 Å2
3---9.352 Å2
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11546 0 0 0 11546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.45
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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