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- PDB-6q19: Inferred intermediate (I-6) of the human antibody lineage 652 -

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Basic information

Entry
Database: PDB / ID: 6q19
TitleInferred intermediate (I-6) of the human antibody lineage 652
Components
  • Fab heavy chain
  • Fab lambda 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: 1.58 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 3, 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 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,6622
Polymers48,6622
Non-polymers00
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-26 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.770, 70.030, 65.650
Angle α, β, γ (deg.)90.000, 108.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab lambda 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)
#2: 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M sodium chloride, 30% (w/v) PEG 8000, 100 mM HEPES pH7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.58→46.573 Å / Num. obs: 55518 / % possible obs: 98.55 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06087 / Net I/σ(I): 14.25
Reflection shellResolution: 1.58→1.637 Å / Rmerge(I) obs: 0.6714 / Num. unique obs: 4982 / CC1/2: 0.517 / % possible all: 89.19

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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: 1.58→46.573 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.03
RfactorNum. reflection% reflection
Rfree0.191 2750 4.95 %
Rwork0.1639 --
obs0.1652 55506 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.62 Å2 / Biso mean: 23.0535 Å2 / Biso min: 8.95 Å2
Refinement stepCycle: final / Resolution: 1.58→46.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 541 3847
Biso mean---34.51 -
Num. residues----445
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.60730.28451200.2748228886
1.6073-1.63650.26811490.2611242492
1.6365-1.6680.27871280.2538257596
1.668-1.7020.25441480.23352654100
1.702-1.7390.22641470.22152667100
1.739-1.77950.21771280.20252666100
1.7795-1.8240.25051220.19192672100
1.824-1.87330.19271400.17612652100
1.8733-1.92840.20431460.17222677100
1.9284-1.99070.17161290.16292687100
1.9907-2.06180.19991360.162652100
2.0618-2.14440.16791490.15492634100
2.1444-2.2420.19731630.14722647100
2.242-2.36020.19971410.16172679100
2.3602-2.5080.1971320.16132698100
2.508-2.70170.20351370.17342662100
2.7017-2.97350.20331200.1542710100
2.9735-3.40370.17361570.14792667100
3.4037-4.28780.14811430.1331267299
4.2878-46.50.17681150.15512773100
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)
13.3828-0.828-0.95262.87780.54383.01130.1315-0.2390.38660.1444-0.0108-0.3372-0.18130.2678-0.08780.1876-0.02880.02390.1686-0.01710.219378.3072-1.0321-22.4535
21.81610.0911-0.64441.8240.22652.04940.02990.05660.0347-0.0540.0053-0.0615-0.1012-0.035-0.02380.08620.0135-0.00090.09440.01150.083773.6327-8.056-27.7583
31.07520.3075-1.4871.698-0.86322.14770.00650.0813-0.07690.0315-0.0416-0.126-0.0448-0.04540.05910.133-0.0124-0.02860.13750.00310.128948.3487-9.01832.7004
41.5911-0.0347-1.2431.9554-0.26062.2619-0.0192-0.00540.0683-0.09080.0253-0.1490.03580.06640.01380.1048-0.0072-0.00920.11250.00360.110754.1025-5.63616.0572
58.02414.7723-3.9123.4509-3.07944.5556-0.0533-0.05230.6072-0.27070.09540.22580.0832-0.0473-0.0680.15720.00390.00150.12110.00220.174148.92170.94577.4663
61.9188-0.1281-0.00732.3721-1.34953.9773-0.101-0.1279-0.1583-0.02940.19670.25150.1432-0.573-0.12760.1452-0.01520.02340.1662-0.00620.216964.0266-29.4175-16.8351
71.1293-0.2799-0.27631.3356-0.45681.2073-0.04290.1051-0.1736-0.1472-0.01880.02920.12870.02460.05570.13340.00220.0040.1194-0.00990.138571.1531-27.4454-25.4839
84.37570.02541.93421.64650.1442.9923-0.04190.132-0.476-0.2210.01550.01870.2053-0.0885-0.00880.2219-0.00310.04010.1536-0.02620.225969.1807-34.8078-24.3174
90.8518-0.5439-0.20751.1497-0.43151.52290.03710.1038-0.1106-0.1756-0.074-0.01590.08010.07880.07470.12810.0047-0.01320.1325-0.00980.126273.756-21.8207-29.5316
101.88380.3763-1.59850.55550.47422.6539-0.2206-0.1553-0.2530.0501-0.0612-0.14480.1240.06510.10520.0970.02350.01080.12550.02870.159362.5817-27.0898-6.8128
111.64780.87070.01181.0713-0.92661.4195-0.1816-0.24810.32910.35940.23390.3766-0.5378-0.2487-0.06310.26310.0822-0.02350.1743-0.03330.203740.8313-9.77410.4454
121.4652-1.4297-0.15781.66020.06170.7167-0.0070.10750.1603-0.0779-0.05050.0233-0.0545-0.03910.0050.1190.0071-0.02480.13340.01180.121350.0672-18.3091-5.504
131.4687-0.8864-0.60353.31820.46320.2492-0.1876-0.0390.26040.09910.1205-0.2603-0.272-0.02820.0710.1304-0.0053-0.00290.1577-0.00620.152354.2111-14.4272-4.5061
142.9977-1.95080.5972.4108-0.4410.83180.03070.0854-0.1086-0.1538-0.0450.1876-0.0198-0.09070.01240.11920.0096-0.02640.1621-0.01580.106544.3795-16.0163-7.5161
153.0027-0.22432.34243.8944-1.60462.3503-0.0199-0.174-0.08410.2568-0.09190.57090.0383-0.29940.10970.0985-0.03140.02590.1364-0.03270.181840.4827-21.5476-3.7502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 24 )L1 - 24
2X-RAY DIFFRACTION2chain 'L' and (resid 25 through 110 )L25 - 110
3X-RAY DIFFRACTION3chain 'L' and (resid 111 through 133 )L111 - 133
4X-RAY DIFFRACTION4chain 'L' and (resid 134 through 201 )L134 - 201
5X-RAY DIFFRACTION5chain 'L' and (resid 202 through 213 )L202 - 213
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 17 )H1 - 17
7X-RAY DIFFRACTION7chain 'H' and (resid 18 through 64 )H18 - 64
8X-RAY DIFFRACTION8chain 'H' and (resid 65 through 83 )H65 - 83
9X-RAY DIFFRACTION9chain 'H' and (resid 84 through 120 )H84 - 120
10X-RAY DIFFRACTION10chain 'H' and (resid 121 through 136 )H121 - 136
11X-RAY DIFFRACTION11chain 'H' and (resid 137 through 151 )H137 - 151
12X-RAY DIFFRACTION12chain 'H' and (resid 152 through 174 )H152 - 174
13X-RAY DIFFRACTION13chain 'H' and (resid 175 through 192 )H175 - 192
14X-RAY DIFFRACTION14chain 'H' and (resid 193 through 220 )H193 - 220
15X-RAY DIFFRACTION15chain 'H' and (resid 221 through 233 )H221 - 233

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