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- PDB-6wiy: Crystal structure of Fab 54-1G05 -

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Basic information

Entry
Database: PDB / ID: 6wiy
TitleCrystal structure of Fab 54-1G05
Components
  • Fab 54-1G05 heavy chain
  • Fab 54-1G05 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: 1.65 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI139445 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: Convergent Evolution in Breadth of Two VH6-1-Encoded Influenza Antibody Clonotypes from a Single Donor.
Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / ...Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / McDermott, A.B. / Wilson, I.A.
History
DepositionApr 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 54-1G05 heavy chain
L: Fab 54-1G05 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1977
Polymers48,7372
Non-polymers4605
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-26 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.909, 79.092, 107.645
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11H-653-

HOH

21L-667-

HOH

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Components

#1: Antibody Fab 54-1G05 heavy chain


Mass: 24971.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 54-1G05 light chain


Mass: 23765.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 8000, 0.2 M NaCl, and 0.1 M phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 62699 / % possible obs: 99.3 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 0.639 / Net I/σ(I): 4.9 / Num. measured all: 802134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.7112.30.86261060.8390.2520.8990.45498.3
1.71-1.7813.10.62561510.9240.1770.650.47398.6
1.78-1.8612.90.44661510.9620.1270.4640.50298.7
1.86-1.9612.30.30161940.9790.0880.3140.56798.9
1.96-2.0812.70.20762280.990.060.2150.59399.3
2.08-2.2413.30.15262150.9940.0430.1580.61799.3
2.24-2.4612.70.11662810.9960.0340.1210.63999.7
2.46-2.8213.10.08463320.9980.0240.0870.68299.8
2.82-3.5512.90.05463860.9990.0160.0560.797100
3.55-5012.60.03866550.9990.0110.041.028100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQH

4fqh


Resolution: 1.65→48.258 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 3082 4.92 %
Rwork0.1578 59570 -
obs0.1593 62652 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.12 Å2 / Biso mean: 31.0469 Å2 / Biso min: 13.25 Å2
Refinement stepCycle: final / Resolution: 1.65→48.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 70 629 4068
Biso mean--66.96 42.72 -
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 (%)
1.6504-1.67620.29721260.2484251894
1.6762-1.70360.24121620.2284262798
1.7036-1.7330.23641380.2017266798
1.733-1.76450.19251200.1898264598
1.7645-1.79850.22761300.1909270399
1.7985-1.83520.22391220.1756266999
1.8352-1.87510.21021340.1713266799
1.8751-1.91870.20151470.166268699
1.9187-1.96670.19941320.1577269999
1.9667-2.01990.18141690.1571264199
2.0199-2.07930.1931360.1591270399
2.0793-2.14640.19371520.16232666100
2.1464-2.22310.21531240.162273099
2.2231-2.31220.22261460.16512695100
2.3122-2.41740.18511500.16722719100
2.4174-2.54480.2051350.16912751100
2.5448-2.70430.1831340.17112732100
2.7043-2.9130.20181330.16742775100
2.913-3.20610.19371370.1582760100
3.2061-3.66990.17281530.14482758100
3.6699-4.62310.1451380.1232821100
4.6231-48.2580.17731640.15072938100
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)
11.42490.4091-0.13120.8069-0.22320.9404-0.0051-0.0539-0.0654-0.0073-0.01520.02370.1805-0.00150.0330.16140.01090.0110.12470.00390.148912.5606-14.330312.9974
21.9394-0.3306-0.63731.87840.94254.1718-0.09-0.37680.10720.39610.0738-0.19040.05910.1784-0.00820.15910.0115-0.0560.2361-0.03480.17725.21287.863924.2495
31.27570.37290.00623.63121.26452.4509-0.01530.0199-0-0.0689-0.02470.16890.028-0.17540.04220.1089-0.002-0.00410.13240.00280.1331-6.1519-2.918414.571
43.36960.067-1.09721.78750.2041.69080.01280.00430.2621-0.04690.052-0.3366-0.2150.219-0.03930.1757-0.0297-0.01320.1925-0.03580.232221.854422.29117.126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 1:131)H1 - 131
2X-RAY DIFFRACTION2(chain H and resid 132:213)H132 - 213
3X-RAY DIFFRACTION3(chain L and resid 1:108)L1 - 108
4X-RAY DIFFRACTION4(chain L and resid 109:213)L109 - 213

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