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- PDB-6q1k: Inferred intermediate I-7 of the human antibody lineage 652 -

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Basic information

Entry
Database: PDB / ID: 6q1k
TitleInferred intermediate I-7 of the human antibody lineage 652
Components
  • Fab heavy chain
  • Fab lambda light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117892 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Affinity maturation in a human humoral response to influenza hemagglutinin.
Authors: McCarthy, K.R. / Raymond, D.D. / Do, K.T. / Schmidt, A.G. / Harrison, S.C.
History
DepositionAug 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab lambda light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,6622
Non-polymers921
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-24 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.160, 69.990, 65.230
Angle α, β, γ (deg.)90.000, 108.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab heavy chain


Mass: 25731.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human)
#2: Antibody Fab lambda light chain


Mass: 22930.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200mM sodium acetate, 30% (w/v) PEG 400, 100mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.334 Å / Num. obs: 20469 / % possible obs: 99.54 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0946 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 2025 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.334 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.29
RfactorNum. reflection% reflection
Rfree0.2394 1015 4.96 %
Rwork0.191 --
obs0.1934 20461 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.04 Å2 / Biso mean: 26.6117 Å2 / Biso min: 9.08 Å2
Refinement stepCycle: final / Resolution: 2.2→46.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 6 241 3535
Biso mean--41.55 31.94 -
Num. residues----441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.31610.31171510.2356275499
2.3161-2.46120.29361280.22362787100
2.4612-2.65130.28141470.22112748100
2.6513-2.9180.2521280.19822803100
2.918-3.34020.24531470.18772785100
3.3402-4.20780.2271350.1647278799
4.2078-46.30.1971790.1784278299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8775-0.17010.34971.2158-0.47121.51440.05140.0866-0.0823-0.1104-0.03620.09370.08290.0238-0.00190.1587-0.00140.00420.1669-0.02180.178169.9456-27.4373-25.3511
21.4304-0.1912-0.06740.9152-0.28191.0119-0.0725-0.2269-0.07980.110.07350.1094-0.14060.1080.02870.2289-0.0082-0.04410.1629-0.01530.15851.0176-18.9557-3.205
31.8077-1.0128-0.51632.21380.2560.8020.09990.1210.0318-0.2096-0.11140.0089-0.0231-0.01540.03830.19650.0059-0.01270.20010.00530.1847.0541-17.5516-5.8022
41.5631-0.2471-0.59071.2157-0.36171.2892-0.00340.02260.0275-0.0174-0.0153-0.0842-0.02060.01490.01080.1842-0.0022-0.00690.1525-0.00560.15773.7938-7.0593-27.2372
50.94240.0694-1.0016-0.1076-0.15320.94910.0528-0.13670.00660.0442-0.0034-0.0406-0.06680.0963-0.05320.1964-0.0344-0.01430.1972-0.00760.201356.0458-8.469-4.5133
61.69270.0473-0.04422.3417-0.31471.3251-0.0098-0.04560.0906-0.0491-0.0125-0.1433-0.10170.04750.03610.1901-0.01180.00030.184-0.01580.188552.4992-5.08146.3263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 120 )H1 - 120
2X-RAY DIFFRACTION2chain 'H' and (resid 121 through 151 )H121 - 151
3X-RAY DIFFRACTION3chain 'H' and (resid 152 through 231 )H152 - 231
4X-RAY DIFFRACTION4chain 'L' and (resid 3 through 97 )L3 - 97
5X-RAY DIFFRACTION5chain 'L' and (resid 98 through 132 )L98 - 132
6X-RAY DIFFRACTION6chain 'L' and (resid 133 through 212 )L133 - 212

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