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- PDB-5eor: Structure of the murine antibody Fab 8E3 bound to the vaccinia vi... -

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Basic information

Entry
Database: PDB / ID: 5eor
TitleStructure of the murine antibody Fab 8E3 bound to the vaccinia virus A27 peptide 101-110
Components
  • Protein A27
  • anti vaccinia virus A27 antibody 8E3 heavy chain
  • anti vaccinia virus A27 antibody 8E3 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / Fab / vaccinia virus / neutralizing / linear epitope / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyChordopoxvirus fusion protein/multifunctional envelope protein A27 / Chordopoxvirus multifunctional envelope protein A27 / fusion of virus membrane with host plasma membrane / Immunoglobulins / viral envelope / Immunoglobulin-like / Sandwich / Mainly Beta / Protein OPG154
Function and homology information
Biological speciesMus musculus (house mouse)
Vaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsMatho, M.H. / Zajonc, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200900048C United States
CitationJournal: J.Virol. / Year: 2016
Title: Linear Epitopes in Vaccinia Virus A27 Are Targets of Protective Antibodies Induced by Vaccination against Smallpox.
Authors: Kaever, T. / Matho, M.H. / Meng, X. / Crickard, L. / Schlossman, A. / Xiang, Y. / Crotty, S. / Peters, B. / Zajonc, D.M.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti vaccinia virus A27 antibody 8E3 heavy chain
L: anti vaccinia virus A27 antibody 8E3 light chain
A: Protein A27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7454
Polymers47,7223
Non-polymers231
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-42 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.250, 118.250, 198.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody anti vaccinia virus A27 antibody 8E3 heavy chain


Mass: 23028.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody anti vaccinia virus A27 antibody 8E3 light chain


Mass: 23471.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Protein A27


Mass: 1222.308 Da / Num. of mol.: 1 / Fragment: UNP residues 101-110 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus / References: UniProt: P11258*PLUS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 3000, 200 mM magnesium chloride, 100 mM cacodylate ph 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→55.62 Å / Num. obs: 35641 / % possible obs: 97.8 % / Redundancy: 2.5 % / Rsym value: 0.095 / Net I/σ(I): 6.3
Reflection shellResolution: 2.27→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.1 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0104refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NTF

2ntf


Resolution: 2.27→55.62 Å / SU B: 4.657 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22363 1885 5 %RANDOM
Rwork0.20296 ---
obs0.20399 35641 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.313 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.27→55.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 1 206 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223414
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9514658
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4424.252127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48515533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4881512
X-RAY DIFFRACTIONr_chiral_restr0.080.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 229 -
Rwork0.31 4700 -
obs--98.84 %

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