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- PDB-5eoq: Structure of the murine Fab 1G6 bound to the vaccinia virus A27 p... -

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Basic information

Entry
Database: PDB / ID: 5eoq
TitleStructure of the murine Fab 1G6 bound to the vaccinia virus A27 peptide 31-40
Components
  • Anti vaccinia virus A27 antibody Fab 1G6 heavy chain
  • Anti vaccinia virus A27 antibody Fab 1G6 light chain
  • Protein A27
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: 1.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Anti vaccinia virus A27 antibody Fab 1G6 heavy chain
L: Anti vaccinia virus A27 antibody Fab 1G6 light chain
A: Protein A27


Theoretical massNumber of molelcules
Total (without water)48,6853
Polymers48,6853
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-29 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.339, 99.339, 117.564
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Antibody Anti vaccinia virus A27 antibody Fab 1G6 heavy chain


Mass: 23577.332 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 Fab 1G6 light chain


Mass: 23946.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Protein A27


Mass: 1161.328 Da / Num. of mol.: 1 / Fragment: UNP residues 31-40 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus / References: UniProt: P11258
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 4000, 200 mM sodium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→49.67 Å / Num. obs: 45752 / % possible obs: 95.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2 / % possible all: 96

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.6.0104refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOR

5eor


Resolution: 1.95→49.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.667 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 2323 5.1 %RANDOM
Rwork0.1974 ---
obs0.1993 43427 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.41 Å2 / Biso mean: 32.467 Å2 / Biso min: 17.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.95→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 0 398 3782
Biso mean---40.83 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223468
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9494727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35324.436133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79815553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4771512
X-RAY DIFFRACTIONr_chiral_restr0.0780.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212593
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 177 -
Rwork0.321 3161 -
all-3338 -
obs--95.89 %

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