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- PDB-6q1j: Antibody H2227 from the human antibody lineage 652 -

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Basic information

Entry
Database: PDB / ID: 6q1j
TitleAntibody H2227 from the human antibody lineage 652
Components
  • Fab heavy chainFragment antigen-binding
  • 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: 2.703 Å
AuthorsMcCarthy, K.R. / Harrison, S.C. / Raymond, D.D.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4542
Polymers48,4542
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-25 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.300, 69.380, 142.820
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 Fab heavy chain / Fragment antigen-binding


Mass: 25679.598 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: 22774.102 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)

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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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100mM ammonium sulfate, 40% (v/v) PEG 400, 100mM sodium citrate pH 4.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→44.691 Å / Num. obs: 15536 / % possible obs: 95.77 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1392 / Net I/σ(I): 13.65
Reflection shellResolution: 2.7→44.18 Å / Rmerge(I) obs: 0.9699 / Num. unique obs: 1530 / CC1/2: 0.703 / % possible all: 95.98

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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: 2.703→44.691 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2456 763 4.91 %
Rwork0.2252 --
obs0.2263 15530 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.54 Å2 / Biso mean: 42.7153 Å2 / Biso min: 24.19 Å2
Refinement stepCycle: final / Resolution: 2.703→44.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 0 0 3298
Num. residues----443
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7032-2.91190.4041740.3404293598
2.9119-3.20480.27891650.2589298399
3.2048-3.66840.25741440.2466296997
3.6684-4.6210.20181490.1873292395
4.621-44.6910.20661310.197295791
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)
10.20920.1161-0.3130.1826-0.32350.7064-0.07210.6197-0.5391-0.2360.1024-0.57350.21160.0956-0.02170.3786-0.0109-0.00420.4741-0.020.54794.8641-1.651-12.7959
20.82080.12910.4821.43630.62920.66240.13420.0525-0.33730.1069-0.21790.16030.2414-0.036500.2957-0.02550.00410.3940.01840.367.16790.761-1.2727
30.17660.090.0670.28610.01620.5484-0.0934-0.2285-0.80360.0065-0.0515-0.20540.4490.0454-0.01560.4313-0.0105-0.06750.41680.10170.55527.4147-6.8324-3.5768
40.5381-0.01150.78360.64051.28370.4803-0.0648-0.2475-0.09480.05470.04560.08580.1146-0.13480.00140.263-0.0354-0.02450.41470.06790.32218.79336.38732.7351
51.5931-0.79940.090.3554-0.00490.1728-0.4981-0.3495-0.1602-0.09270.13060.1155-0.396-0.1333-0.06080.4747-0.11640.03240.3951-0.10630.3234-2.40150.8256-19.9158
60.3241-0.44981.04182.01930.30350.66310.16740.01110.302-0.2207-0.03670.10770.0410.089800.4821-0.0311-0.00970.3525-0.00420.35192.951214.2929-32.8931
72.2341-0.10050.52070.68181.00651.48370.5452-0.1090.0443-0.5563-0.3227-0.18440.60020.22170.47190.53570.10090.06390.2947-0.0310.3218.51927.6324-36.385
81.0412-1.20090.08160.68030.38760.4727-0.0732-0.33990.05430.71470.08120.1338-0.2913-0.0963-0.00060.42960.0288-0.01420.38920.05270.39330.071723.67273.8392
91.8601-1.2611.20581.66620.21521.1968-0.1479-0.07320.10370.11040.0505-0.103-0.1196-0.0784-0.00010.2801-0.0113-0.01490.35850.0180.32178.72220.08671.3891
100.2789-0.40.09570.5934-0.04740.89480.08650.0345-0.0278-0.31620.06240.12290.05990.13360.14990.3984-0.0189-0.07920.3218-0.00580.3948-1.750320.1234-25.4958
110.563-0.7226-0.80022.01060.17861.6974-0.0027-0.0862-0.0996-0.3790.04060.43490.0788-0.18920.01760.407-0.0457-0.10280.3380.01780.3635-8.953223.533-34.06
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )H1 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 64 )H18 - 64
3X-RAY DIFFRACTION3chain 'H' and (resid 65 through 83 )H65 - 83
4X-RAY DIFFRACTION4chain 'H' and (resid 84 through 120 )H84 - 120
5X-RAY DIFFRACTION5chain 'H' and (resid 121 through 136 )H121 - 136
6X-RAY DIFFRACTION6chain 'H' and (resid 137 through 205 )H137 - 205
7X-RAY DIFFRACTION7chain 'H' and (resid 206 through 231 )H206 - 231
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 29 )L1 - 29
9X-RAY DIFFRACTION9chain 'L' and (resid 30 through 97 )L30 - 97
10X-RAY DIFFRACTION10chain 'L' and (resid 98 through 132 )L98 - 132
11X-RAY DIFFRACTION11chain 'L' and (resid 133 through 212 )L133 - 212

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