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- PDB-5w6c: UCA Fab (unbound) from 6649 Lineage -

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Basic information

Entry
Database: PDB / ID: 5w6c
TitleUCA Fab (unbound) from 6649 Lineage
Components
  • UCA Fab heavy chain
  • UCA Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / FAB / Influenza H1N1
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / immune response / extracellular space / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.634 Å
AuthorsRaymond, D.D. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody.
Authors: Raymond, D.D. / Bajic, G. / Ferdman, J. / Suphaphiphat, P. / Settembre, E.C. / Moody, M.A. / Schmidt, A.G. / Harrison, S.C.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: UCA Fab heavy chain
L: UCA Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,1552
Polymers48,1552
Non-polymers00
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-26 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.640, 66.920, 100.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody UCA Fab heavy chain


Mass: 25308.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B2B6
#2: Antibody UCA Fab light chain


Mass: 22847.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6GMX4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 26% PEG2000 MME, 150 mM ammonium sulfate, 100 mM sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.999919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2016
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999919 Å / Relative weight: 1
ReflectionResolution: 1.63→46.116 Å / Num. obs: 52465 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 6.629 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 1.048 / Net I/σ(I): 27.48 / Num. measured all: 347776 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.63-1.733.2630.5093.0370930.8480.59581.5
1.73-1.857.0550.3318.281430.9720.357100
1.85-27.2320.13816.1276510.9940.149100
2-2.197.2760.07625.8969410.9970.082100
2.19-2.457.2960.05134.3463480.9990.055100
2.45-2.837.2760.03941.656100.9990.042100
2.83-3.467.1130.03249.847420.9990.034100
3.46-4.886.8420.02558.6737500.9990.02799.9
4.88-46.1166.7750.02165.46218710.02399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H42

3h42


Resolution: 1.634→46.116 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2623 5 %Random Selection
Rwork0.1769 ---
obs0.1781 52451 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.68 Å2 / Biso mean: 18.8155 Å2 / Biso min: 7.74 Å2
Refinement stepCycle: final / Resolution: 1.634→46.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 0 442 3705
Biso mean---26.05 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063354
X-RAY DIFFRACTIONf_angle_d0.9474589
X-RAY DIFFRACTIONf_chiral_restr0.057519
X-RAY DIFFRACTIONf_plane_restr0.005583
X-RAY DIFFRACTIONf_dihedral_angle_d12.5171982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.634-1.66370.3645800.36311628170862
1.6637-1.69570.29311370.25692481261894
1.6957-1.73030.25841400.226626452785100
1.7303-1.7680.24851400.206826812821100
1.768-1.80910.23821380.20126442782100
1.8091-1.85430.24361430.199626512794100
1.8543-1.90450.22391340.193526322766100
1.9045-1.96050.21991400.177726522792100
1.9605-2.02380.21861420.17526702812100
2.0238-2.09610.21861390.167826742813100
2.0961-2.18010.20071410.176426652806100
2.1801-2.27930.19231450.172626822827100
2.2793-2.39940.18631370.173526722809100
2.3994-2.54980.2311420.18226782820100
2.5498-2.74660.21891410.187427002841100
2.7466-3.0230.19451440.183727182862100
3.023-3.46030.1871430.173527172860100
3.4603-4.3590.17831440.147327522896100
4.359-46.13460.15371530.155528863039100

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