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- PDB-4hha: Anti-Human Cytomegalovirus (HCMV) Fab KE5 with epitope peptide AD-2S1 -

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Basic information

Entry
Database: PDB / ID: 4hha
TitleAnti-Human Cytomegalovirus (HCMV) Fab KE5 with epitope peptide AD-2S1
Components
  • Antibody KE5
  • Fab KE5
  • Glycoprotein B
KeywordsIMMUNE SYSTEM / Fab fragment / Antibody
Function / homologyHerpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Glycoprotein B
Function and homology information
Biological speciesHomo sapiens (human)
Human herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBryson, S. / Risnes, L. / Damgupta, S. / Thomson, C.A. / Pfoh, R. / Schrader, J.W. / Pai, E.F.
CitationJournal: J. Immunol. / Year: 2016
Title: Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation.
Authors: Bryson, S. / Thomson, C.A. / Risnes, L.F. / Dasgupta, S. / Smith, K. / Schrader, J.W. / Pai, E.F.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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
A: Fab KE5
B: Antibody KE5
P: Glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2958
Polymers50,1183
Non-polymers1775
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-84 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.250, 65.510, 67.110
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab KE5


Mass: 23471.064 Da / Num. of mol.: 1 / Fragment: Fab fragment KE5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Antibody KE5


Mass: 25400.516 Da / Num. of mol.: 1 / Fragment: AD-2S1 eptiope / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide Glycoprotein B


Mass: 1246.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Human herpesvirus 5 / References: UniProt: Q9YKI2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 1.88 Å3/Da / Density % sol: 34.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.05M Na Acetate, pH 4.2, 18% Jeffamine 1500, 0.2M Ammonium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 28, 2012 / Details: Toroidal focusing mirror
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→43 Å / Num. all: 49164 / Num. obs: 48944 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.72 % / Rmerge(I) obs: 0.0478 / Net I/σ(I): 19.84
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.89 / Num. unique all: 4260 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
CNSrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HH9

4hh9


Resolution: 1.6→43 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 2433 RANDOM
Rwork0.213 --
all0.213 49142 -
obs0.213 48580 -
Refinement stepCycle: LAST / Resolution: 1.6→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 5 289 3725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005857
X-RAY DIFFRACTIONc_angle_d1.60017

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