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- PDB-3esv: Crystal structure of the engineered neutralizing antibody M18 -

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Basic information

Entry
Database: PDB / ID: 3esv
TitleCrystal structure of the engineered neutralizing antibody M18
ComponentsAntibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker
KeywordsIMMUNE SYSTEM / single-chain FV / monoclonal antibody / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 6, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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


Theoretical massNumber of molelcules
Total (without water)53,7332
Polymers53,7332
Non-polymers00
Water5,152286
1
F: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker


Theoretical massNumber of molelcules
Total (without water)26,8671
Polymers26,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker


Theoretical massNumber of molelcules
Total (without water)26,8671
Polymers26,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.070, 54.210, 61.950
Angle α, β, γ (deg.)71.80, 75.58, 71.25
Int Tables number1
Space group name H-MP1
DetailsAsymmetric unit contains two 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.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 4000, 0.1 M HEPES, 10% Isopropanol, 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: Sep 24, 2004 / 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: 2→50 Å / Num. all: 26245 / Num. obs: 26245 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Χ2: 0.968 / Net I/σ(I): 26.4
Reflection shellResolution: 2→2.08 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.107 / Num. unique all: 2514 / Χ2: 1.017 / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ESU

3esu


Resolution: 2→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.865 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1270 4.5 %random
Rwork0.194 ---
all0.194 25286 --
obs0.194 25286 90 %-
Solvent computationBsol: 52.192 Å2
Displacement parametersBiso max: 41.87 Å2 / Biso mean: 17.324 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1--5.395 Å20.215 Å2-1.05 Å2
2--2.699 Å21.703 Å2
3---2.696 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 0 286 3807
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_scbond_it1.8892
X-RAY DIFFRACTIONc_mcangle_it1.7092
X-RAY DIFFRACTIONc_scangle_it2.6222.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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