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- PDB-4hh9: Anti-Human Cytomegalovirus (HCMV) Fab KE5 -

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Basic information

Entry
Database: PDB / ID: 4hh9
TitleAnti-Human Cytomegalovirus (HCMV) Fab KE5
Components
  • Fab KE5, heavy chain
  • Fab KE5, light chain
KeywordsIMMUNE SYSTEM / Fab / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab KE5, light chain
B: Fab KE5, heavy chain
C: Fab KE5, light chain
D: Fab KE5, heavy chain


Theoretical massNumber of molelcules
Total (without water)97,7434
Polymers97,7434
Non-polymers00
Water12,376687
1
A: Fab KE5, light chain
B: Fab KE5, heavy chain


Theoretical massNumber of molelcules
Total (without water)48,8722
Polymers48,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-23 kcal/mol
Surface area19670 Å2
MethodPISA
2
C: Fab KE5, light chain
D: Fab KE5, heavy chain


Theoretical massNumber of molelcules
Total (without water)48,8722
Polymers48,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-25 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.860, 79.470, 86.270
Angle α, β, γ (deg.)90.00, 113.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab KE5, light chain


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


Mass: 25400.516 Da / Num. of mol.: 2 / Fragment: KE5 Heavy Chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.05M Bis-Tris, pH 5.5, 20% PEG 3350, 0.2M Ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: 1.7→43 Å / Num. all: 100764 / Num. obs: 97584 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.33 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.04
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 7.37 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.8 / Num. unique all: 7970 / % possible all: 95.5

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Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
CNSrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EYF

3eyf


Resolution: 1.7→43 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.224 4766 RANDOM
Rwork0.217 --
all0.217 100740 -
obs0.217 95831 -
Refinement stepCycle: LAST / Resolution: 1.7→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6744 0 0 687 7431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00412
X-RAY DIFFRACTIONc_angle_d1.36103

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